| geneid | 19 |
|---|---|
| ensemblid | ENSG00000165029.17 |
| hgncid | 29 |
| symbol | ABCA1 |
| name | ATP binding cassette subfamily A member 1 |
| refseq_nuc | NM_005502.4 |
| refseq_prot | NP_005493.2 |
| ensembl_nuc | ENST00000374736.8 |
| ensembl_prot | ENSP00000363868.3 |
| mane_status | MANE Select |
| chr | chr9 |
| start | 104781006 |
| end | 104928155 |
| strand | - |
| ver | v1.2 |
| region | chr9:104781006-104928155 |
| region5000 | chr9:104776006-104933155 |
| regionname0 | ABCA1_chr9_104781006_104928155 |
| regionname5000 | ABCA1_chr9_104776006_104933155 |
| chr:pos | ref | alt | af | annotation | impact | samples | AHAPIDS | ACHAPIDS | ACTHAPIDS | ACTGHAPIDS | ac | an | len | genename | geneid | featuretype | featureid | transcript_biotype | rank | hgvs_c | hgvs_p | cdna_pos_length | cds_pos_length | aa_pos_length | distance | status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr9:104800523
|
T | C | 0.4748 | missense_variant | MODERATE | HG00099.hp1 HG00099.hp2 HG00408.hp1 others(148): Show |
a0001a0003a0006others(12): Show | a0001c0001a0001c0005a0001c0035others(32): Show | a0001c0001t0001a0001c0001t0002a0001c0001t0003others(80): Show | a0001c0001t0001g0016a0001c0001t0001g0026a0001c0001t0001g0077others(148): Show | 151 | 318 | 0 | ABCA1 | ENSG00000165029.17 | transcript | ENST00000374736.8 | protein_coding | 35/50 | c.4760A>G | p.Lys1587Arg | 5073/10408 | 4760/6786 | 1587/2261 | ||
|
chr9:104824472
|
T | C | 0.4560 | missense_variant | MODERATE | HG00099.hp2 HG00408.hp2 HG00423.hp2 others(142): Show |
a0002a0003a0006others(14): Show | a0002c0011a0002c0015a0002c0017others(49): Show | a0002c0011t0004a0002c0011t0007a0002c0011t0012others(99): Show | a0002c0011t0004g0112a0002c0011t0004g0213a0002c0011t0004g0263others(142): Show | 145 | 318 | 0 | ABCA1 | ENSG00000165029.17 | transcript | ENST00000374736.8 | protein_coding | 18/50 | c.2649A>G | p.Ile883Met | 2962/10408 | 2649/6786 | 883/2261 | ||
|
chr9:104825752
|
C | T | 0.1541 | missense_variant | MODERATE | HG00408.hp2 HG00558.hp2 HG00609.hp2 others(46): Show |
a0006a0007a0013others(1): Show | a0006c0004a0006c0012a0006c0063others(7): Show | a0006c0004t0002a0006c0004t0003a0006c0004t0004others(31): Show | a0006c0004t0002g0132a0006c0004t0002g0133a0006c0004t0003g0190others(46): Show | 49 | 318 | 0 | ABCA1 | ENSG00000165029.17 | transcript | ENST00000374736.8 | protein_coding | 17/50 | c.2473G>A | p.Val825Ile | 2786/10408 | 2473/6786 | 825/2261 |
| genename | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
ahapid | alen | total | AFR | AMR | EAS | EUR | SAS | aseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ABCA1 | 0/0 | a0006 | 2261 | 20 | 0 | 4 | 16 | 0 | 0 | subcellular location copy fasta | chr9 | 104776006 | 104933155 |
Click to load Haplotype QTL data...
| pos | S. Strand |
E# Exon Number |
max | median | min | diff | type | haplotypeid | max_hap_list | min_hap_list | symbol | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 104927935 | - | 1 | -0.6429 | -0.6275 | -0.6063 | 0.0365 | acceptor | a0006 | HG01361.hp2 | NA19010.hp2 NA19011.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104903614 | - | 2 | -0.9943 | -0.9941 | -0.9907 | 0.0037 | acceptor | a0006 | HG00609.hp2 NA18978.hp1 NA18979.hp1 NA18983.hp2 NA18984.hp1 others(2): Show |
NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104903771 | - | 2 | 0.9908 | 0.9902 | 0.9867 | 0.0041 | donor | a0006 | HG01255.hp1 | HG01978.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104889102 | - | 3 | -0.9952 | -0.9947 | -0.9929 | 0.0022 | acceptor | a0006 | NA19011.hp2 | NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104889195 | - | 3 | 0.9924 | 0.9920 | 0.9913 | 0.0011 | donor | a0006 | HG01243.hp1 HG01361.hp2 |
NA19011.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104884427 | - | 4 | -0.9971 | -0.9967 | -0.9967 | 0.0005 | acceptor | a0006 | HG01978.hp2 NA18967.hp1 NA19011.hp2 |
NA19084.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104884568 | - | 4 | 0.9940 | 0.9938 | 0.9931 | 0.0009 | donor | a0006 | HG00558.hp2 | NA19009.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104883039 | - | 5 | -0.9991 | -0.9989 | -0.9988 | 0.0002 | acceptor | a0006 | NA19009.hp2 NA19011.hp2 |
HG00609.hp2 NA19010.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104883157 | - | 5 | 0.9949 | 0.9949 | 0.9947 | 0.0002 | donor | a0006 | HG02027.hp2 | HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104861679 | - | 6 | -0.9990 | -0.9987 | -0.9973 | 0.0017 | acceptor | a0006 | NA18991.hp1 | NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104861800 | - | 6 | 0.9955 | 0.9942 | 0.9896 | 0.0059 | donor | a0006 | NA18967.hp1 | NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104858522 | - | 7 | -0.9984 | -0.9983 | -0.9983 | 0.0001 | acceptor | a0006 | NA19009.hp2 | NA18944.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104858698 | - | 7 | 0.9955 | 0.9952 | 0.9950 | 0.0005 | donor | a0006 | NA19009.hp2 | NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104845477 | - | 8 | -0.9954 | -0.9951 | -0.9951 | 0.0002 | acceptor | a0006 | NA18978.hp1 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 others(12): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104845569 | - | 8 | 0.9952 | 0.9951 | 0.9951 | 0.0001 | donor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 others(11): Show |
NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104840279 | - | 9 | -0.9979 | -0.9978 | -0.9977 | 0.0002 | acceptor | a0006 | NA18955.hp2 | HG01978.hp2 NA18978.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104840519 | - | 9 | 0.9869 | 0.9868 | 0.9865 | 0.0004 | donor | a0006 | HG01255.hp1 | NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104837428 | - | 10 | -0.9992 | -0.9992 | -0.9992 | 0.0000 | acceptor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(11): Show |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104837567 | - | 10 | 0.9989 | 0.9989 | 0.9988 | 0.0001 | donor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(11): Show |
HG01978.hp2 NA18978.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104836980 | - | 11 | -0.9982 | -0.9982 | -0.9980 | 0.0002 | acceptor | a0006 | NA19011.hp2 | NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104837096 | - | 11 | 0.9859 | 0.9851 | 0.9850 | 0.0009 | donor | a0006 | HG01978.hp2 NA18978.hp1 |
NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104832574 | - | 12 | -0.9916 | -0.9915 | -0.9912 | 0.0004 | acceptor | a0006 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104832771 | - | 12 | 0.9871 | 0.9866 | 0.9865 | 0.0005 | donor | a0006 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
NA18984.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104831622 | - | 13 | -0.9972 | -0.9971 | -0.9971 | 0.0001 | acceptor | a0006 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(8): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104831827 | - | 13 | 0.9913 | 0.9912 | 0.9907 | 0.0007 | donor | a0006 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104830925 | - | 14 | -0.9968 | -0.9968 | -0.9962 | 0.0006 | acceptor | a0006 | HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(9): Show |
HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104831101 | - | 14 | 0.9954 | 0.9951 | 0.9937 | 0.0017 | donor | a0006 | NA18955.hp2 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104828916 | - | 15 | -0.9978 | -0.9978 | -0.9978 | 0.0000 | acceptor | a0006 | HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(4): Show |
NA18978.hp1 NA18991.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104829138 | - | 15 | 0.9971 | 0.9970 | 0.9970 | 0.0001 | donor | a0006 | HG00558.hp2 HG02027.hp2 NA18944.hp2 NA19010.hp2 NA19084.hp2 |
HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(7): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104826948 | - | 16 | -0.9983 | -0.9983 | -0.9981 | 0.0002 | acceptor | a0006 | NA18967.hp1 NA19009.hp2 NA19066.hp2 |
NA18978.hp1 NA18991.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104827169 | - | 16 | 0.9963 | 0.9963 | 0.9952 | 0.0011 | donor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(10): Show |
NA18978.hp1 NA18991.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104825683 | - | 17 | -0.9947 | -0.9945 | -0.9945 | 0.0001 | acceptor | a0006 | NA18978.hp1 NA18991.hp1 |
HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(13): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104825887 | - | 17 | 0.9580 | 0.9580 | 0.9577 | 0.0002 | donor | a0006 | NA18967.hp1 NA19009.hp2 NA19066.hp2 |
NA18978.hp1 NA18991.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104824465 | - | 18 | -0.9990 | -0.9990 | -0.9990 | 0.0000 | acceptor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(15): Show |
HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(15): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104824578 | - | 18 | 0.9975 | 0.9974 | 0.9974 | 0.0000 | donor | a0006 | NA18978.hp1 NA18991.hp1 |
HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(13): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104822496 | - | 19 | -0.9949 | -0.9949 | -0.9948 | 0.0001 | acceptor | a0006 | HG00558.hp2 HG01361.hp2 HG01978.hp2 NA18967.hp1 NA19010.hp2 |
NA19084.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104822667 | - | 19 | 0.9972 | 0.9972 | 0.9972 | 0.0000 | donor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(14): Show |
NA19084.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104821375 | - | 20 | -0.9991 | -0.9991 | -0.9991 | 0.0000 | acceptor | a0006 | NA19084.hp2 | HG00609.hp2 NA18955.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104821506 | - | 20 | 0.9966 | 0.9966 | 0.9963 | 0.0003 | donor | a0006 | HG00558.hp2 HG01361.hp2 HG01978.hp2 NA18967.hp1 NA19010.hp2 |
NA19084.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104819927 | - | 21 | -0.9973 | -0.9972 | -0.9972 | 0.0001 | acceptor | a0006 | HG00558.hp2 HG01361.hp2 HG01978.hp2 |
NA19011.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104820069 | - | 21 | 0.9980 | 0.9979 | 0.9979 | 0.0001 | donor | a0006 | NA19084.hp2 | HG00609.hp2 NA18955.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104819586 | - | 22 | -0.9200 | -0.9176 | -0.9105 | 0.0094 | acceptor | a0006 | HG00558.hp2 HG01361.hp2 HG01978.hp2 |
NA19011.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104819723 | - | 22 | 0.8153 | 0.8138 | 0.8123 | 0.0030 | donor | a0006 | HG01243.hp1 NA18944.hp2 NA18983.hp2 NA18984.hp1 |
HG02027.hp2 NA18979.hp1 NA19009.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104818663 | - | 23 | -0.9983 | -0.9983 | -0.9979 | 0.0004 | acceptor | a0006 | HG00558.hp2 HG01361.hp2 HG01978.hp2 |
HG00609.hp2 NA18955.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104818883 | - | 23 | 0.9966 | 0.9961 | 0.9958 | 0.0008 | donor | a0006 | HG01255.hp1 | HG01243.hp1 NA18944.hp2 NA18983.hp2 NA18984.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104817332 | - | 24 | -0.9827 | -0.9825 | -0.9818 | 0.0009 | acceptor | a0006 | NA18967.hp1 NA19010.hp2 NA19084.hp2 |
NA18978.hp1 NA18991.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104817404 | - | 24 | 0.9833 | 0.9828 | 0.9825 | 0.0008 | donor | a0006 | NA18967.hp1 NA19010.hp2 NA19084.hp2 |
HG00609.hp2 NA18955.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104816143 | - | 25 | -0.9979 | -0.9979 | -0.9979 | 0.0000 | acceptor | a0006 | HG02027.hp2 NA18978.hp1 NA18991.hp1 |
HG01255.hp1 NA18967.hp1 NA19010.hp2 NA19011.hp2 NA19084.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104816345 | - | 25 | 0.9984 | 0.9984 | 0.9984 | 0.0000 | donor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 HG02027.hp2 others(5): Show |
HG01255.hp1 NA18967.hp1 NA19010.hp2 NA19011.hp2 NA19084.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104814427 | - | 26 | -0.9904 | -0.9904 | -0.9904 | 0.0001 | acceptor | a0006 | HG01978.hp2 | NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104814475 | - | 26 | 0.9986 | 0.9986 | 0.9985 | 0.0000 | donor | a0006 | HG01361.hp2 HG02027.hp2 |
HG01978.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104814118 | - | 27 | -0.9936 | -0.9936 | -0.9936 | 0.0000 | acceptor | a0006 | HG02027.hp2 | HG01978.hp2 NA18967.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104814231 | - | 27 | 0.9986 | 0.9986 | 0.9985 | 0.0000 | donor | a0006 | HG02027.hp2 | NA18967.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104812574 | - | 28 | -0.9574 | -0.9564 | -0.9543 | 0.0031 | acceptor | a0006 | NA18944.hp2 NA18983.hp2 NA18984.hp1 |
HG02027.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104812722 | - | 28 | 0.9843 | 0.9779 | 0.9777 | 0.0065 | donor | a0006 | HG02027.hp2 | NA18944.hp2 NA18983.hp2 NA18984.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104810800 | - | 29 | -0.9960 | -0.9956 | -0.9956 | 0.0004 | acceptor | a0006 | NA18944.hp2 NA18983.hp2 NA18984.hp1 |
HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104810924 | - | 29 | 0.9405 | 0.9398 | 0.9382 | 0.0023 | donor | a0006 | HG00609.hp2 NA18979.hp1 |
NA18944.hp2 NA18983.hp2 NA18984.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104809466 | - | 30 | -0.9972 | -0.9972 | -0.9970 | 0.0003 | acceptor | a0006 | HG01255.hp1 NA19009.hp2 NA19010.hp2 NA19011.hp2 NA19066.hp2 others(1): Show |
NA18944.hp2 NA18983.hp2 NA18984.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104809564 | - | 30 | 0.9958 | 0.9957 | 0.9950 | 0.0008 | donor | a0006 | HG00558.hp2 | NA18944.hp2 NA18983.hp2 NA18984.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104806241 | - | 31 | -0.9901 | -0.9894 | -0.9889 | 0.0012 | acceptor | a0006 | NA18979.hp1 | HG01243.hp1 HG01361.hp2 HG01978.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104806430 | - | 31 | 0.9980 | 0.9980 | 0.9978 | 0.0002 | donor | a0006 | NA18978.hp1 NA18991.hp1 |
HG01243.hp1 HG01361.hp2 HG01978.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104804626 | - | 32 | -0.9323 | -0.9255 | -0.9254 | 0.0069 | acceptor | a0006 | NA18979.hp1 | HG00609.hp2 HG02027.hp2 NA18967.hp1 NA19009.hp2 NA19011.hp2 others(1): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104804720 | - | 32 | 0.6057 | 0.6036 | 0.5970 | 0.0087 | donor | a0006 | NA18984.hp1 | NA18979.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104803284 | - | 33 | -0.9981 | -0.9981 | -0.9978 | 0.0003 | acceptor | a0006 | HG00609.hp2 HG02027.hp2 NA18955.hp2 NA18967.hp1 NA18978.hp1 others(5): Show |
NA18979.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104803316 | - | 33 | 0.9983 | 0.9983 | 0.9981 | 0.0002 | donor | a0006 | NA19084.hp2 | NA18979.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104802054 | - | 34 | -0.9978 | -0.9977 | -0.9975 | 0.0003 | acceptor | a0006 | NA19084.hp2 | NA18984.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104802159 | - | 34 | 0.9940 | 0.9938 | 0.9932 | 0.0008 | donor | a0006 | NA19066.hp2 | HG01255.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104800510 | - | 35 | -0.9981 | -0.9980 | -0.9979 | 0.0002 | acceptor | a0006 | NA19066.hp2 | HG00609.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104800584 | - | 35 | 0.9974 | 0.9974 | 0.9970 | 0.0005 | donor | a0006 | NA19066.hp2 | HG01255.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104799819 | - | 36 | -0.9945 | -0.9941 | -0.9931 | 0.0015 | acceptor | a0006 | HG02027.hp2 | NA19066.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104799988 | - | 36 | 0.9985 | 0.9984 | 0.9983 | 0.0002 | donor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18983.hp2 |
NA18984.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104798421 | - | 37 | -0.9980 | -0.9978 | -0.9978 | 0.0002 | acceptor | a0006 | HG02027.hp2 | HG00609.hp2 HG01255.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104798598 | - | 37 | 0.9985 | 0.9984 | 0.9983 | 0.0003 | donor | a0006 | NA18984.hp1 | NA18991.hp1 NA19011.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104796309 | - | 38 | -0.9937 | -0.9935 | -0.9932 | 0.0005 | acceptor | a0006 | NA19066.hp2 | HG02027.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104796424 | - | 38 | 0.9959 | 0.9959 | 0.9958 | 0.0001 | donor | a0006 | NA19066.hp2 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18983.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104796053 | - | 39 | -0.9989 | -0.9989 | -0.9989 | 0.0000 | acceptor | a0006 | HG00609.hp2 HG01255.hp1 NA18955.hp2 NA18967.hp1 NA18978.hp1 others(6): Show |
HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 HG02027.hp2 others(4): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104796197 | - | 39 | 0.9990 | 0.9990 | 0.9990 | 0.0000 | donor | a0006 | NA19066.hp2 | HG00558.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(11): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104794387 | - | 40 | -0.9718 | -0.9718 | -0.9716 | 0.0001 | acceptor | a0006 | HG00609.hp2 HG01255.hp1 NA18955.hp2 NA18967.hp1 NA18978.hp1 others(6): Show |
HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104794510 | - | 40 | 0.9949 | 0.9949 | 0.9949 | 0.0000 | donor | a0006 | HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(14): Show |
HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104793171 | - | 41 | -0.9974 | -0.9974 | -0.9974 | 0.0001 | acceptor | a0006 | HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(12): Show |
HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104793300 | - | 41 | 0.9971 | 0.9970 | 0.9970 | 0.0000 | donor | a0006 | NA19009.hp2 NA19066.hp2 |
HG00558.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104792786 | - | 42 | -0.9990 | -0.9989 | -0.9989 | 0.0001 | acceptor | a0006 | HG00558.hp2 | NA19009.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104792906 | - | 42 | 0.9986 | 0.9985 | 0.9985 | 0.0001 | donor | a0006 | HG00558.hp2 | HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 HG01978.hp2 others(12): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104791936 | - | 43 | -0.9963 | -0.9963 | -0.9963 | 0.0001 | acceptor | a0006 | HG00558.hp2 | NA19009.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104791998 | - | 43 | 0.9991 | 0.9991 | 0.9991 | 0.0000 | donor | a0006 | HG00558.hp2 HG00609.hp2 HG01243.hp1 HG01255.hp1 HG01361.hp2 others(13): Show |
NA19009.hp2 NA19066.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104790922 | - | 44 | -0.9983 | -0.9983 | -0.9983 | 0.0000 | acceptor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18944.hp2 others(3): Show |
HG00609.hp2 HG01255.hp1 HG02027.hp2 NA18955.hp2 NA18967.hp1 others(7): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104791028 | - | 44 | 0.9976 | 0.9976 | 0.9976 | 0.0000 | donor | a0006 | HG00609.hp2 HG01255.hp1 HG02027.hp2 NA18955.hp2 NA18967.hp1 others(6): Show |
NA18983.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104788426 | - | 45 | -0.9994 | -0.9993 | -0.9993 | 0.0000 | acceptor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18944.hp2 others(3): Show |
HG00609.hp2 HG01255.hp1 HG02027.hp2 NA18955.hp2 NA18967.hp1 others(7): Show |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104788567 | - | 45 | 0.9993 | 0.9993 | 0.9993 | 0.0000 | donor | a0006 | NA19084.hp2 | NA18983.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104787920 | - | 46 | -0.9984 | -0.9983 | -0.9983 | 0.0000 | acceptor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18944.hp2 others(3): Show |
NA18967.hp1 NA19009.hp2 NA19011.hp2 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104788054 | - | 46 | 0.9985 | 0.9984 | 0.9984 | 0.0000 | donor | a0006 | HG00558.hp2 HG01243.hp1 HG01361.hp2 HG01978.hp2 NA18944.hp2 others(3): Show |
HG01255.hp1 NA18955.hp2 NA18978.hp1 |
ABCA1 | chr9 | 104776006 | 104933155 |
| 104786873 | - | 47 | -0.9681 | -0.9673 | -0.9672 | 0.0009 | acceptor | a0006 | HG00558.hp2 HG01978.hp2 NA18944.hp2 NA18984.hp1 NA19010.hp2 |
NA19084.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104786976 | - | 47 | 0.9654 | 0.9651 | 0.9650 | 0.0004 | donor | a0006 | HG00558.hp2 HG01978.hp2 NA18944.hp2 NA18984.hp1 NA19010.hp2 |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104786298 | - | 48 | -0.9759 | -0.9756 | -0.9754 | 0.0005 | acceptor | a0006 | HG01243.hp1 | HG01255.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104786390 | - | 48 | 0.9448 | 0.9436 | 0.9425 | 0.0023 | donor | a0006 | NA18955.hp2 | NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104785396 | - | 49 | -0.9981 | -0.9974 | -0.9973 | 0.0008 | acceptor | a0006 | HG01361.hp2 | NA18978.hp1 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104785639 | - | 49 | 0.9964 | 0.9964 | 0.9962 | 0.0002 | donor | a0006 | NA18967.hp1 NA19009.hp2 NA19011.hp2 |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| 104784455 | - | 50 | 0.9911 | 0.9904 | 0.9896 | 0.0015 | donor | a0006 | HG00558.hp2 HG01978.hp2 NA18944.hp2 NA18983.hp2 NA18984.hp1 others(1): Show |
NA18955.hp2 | ABCA1 | chr9 | 104776006 | 104933155 |
| CHR:POS | annotationhgvs_chgvs_p | disease trait-log10podds or beta | AHAPIDS ahapids
|
ACHAPIDS achapids
|
ACTHAPIDS acthapids
|
ACTGHAPIDS actghapids
|
haplotypeids haplotypeids
|
study | initial sample size/replication sample size | report genes | mapped gene | strongest snp risk allele | strand strand
|
impact | chr | ref | alt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr9:104884939
|
c.161-371G>A | HDL cholesterol0.82 | a0001a0002a0003a0004a0005others(24): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(83): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0011others(134): Show | a0001c0001t0001g0082a0001c0001t0001g0088a0001c0001t0003g0089a0001c0001t0003g0211a0001c0001t0003g0297others(162): Show | HG00423.hp1 HG00423.hp2 HG00544.hp1 HG00558.hp1 HG00609.hp1 others(162): Show |
Newly identified loci that influence lipid concent others(44): Show |
8,656 European ancestry individuals/11,437 Europea others(22): Show |
ABCA1 | ABCA1 | rs4149268-C | - | MODIFIER | chr9 | C | T |
|
chr9:104902020
|
c.66+1594G>A | Cholesterol, total2.24 | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Biological, clinical and population relevance of 9 others(24): Show |
100,184 European ancestry individuals/ | ABCA1 | ABCA1 | rs1883025-T | - | MODIFIER | chr9 | C | T |
|
chr9:104902020
|
c.66+1594G>A | HDL cholesterol0.94 | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Biological, clinical and population relevance of 9 others(24): Show |
99,900 European ancestry individuals/ | ABCA1 | ABCA1 | rs1883025-T | - | MODIFIER | chr9 | C | T |
|
chr9:104902020
|
c.66+1594G>A | HDL cholesterol0.08 | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Common variants at 30 loci contribute to polygenic others(14): Show |
19,840 European ancestry individuals/Up to 20,623 others(29): Show |
ABCA1 | ABCA1 | rs1883025-T | - | MODIFIER | chr9 | C | T |
|
chr9:104915008
|
c.-92-11237T>C | Periodontitis (Mean PAL)0.056 | a0001a0002a0003a0004a0005others(9): Show | a0001c0001a0001c0005a0002c0011a0002c0015a0002c0017others(21): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0006a0001c0001t0011a0001c0001t0052others(32): Show | a0001c0001t0001g0088a0001c0001t0001g0102a0001c0001t0001g0121a0001c0001t0001g0238a0001c0001t0001g0291others(44): Show | HG00099.hp1 HG00673.hp1 HG00741.hp1 HG01070.hp2 HG01106.hp1 others(44): Show |
Genome-wide association study of chronic periodont others(36): Show |
up to 4,032 European ancestry individuals/ | ABCA1 | ABCA1 | rs4149263-A | - | MODIFIER | chr9 | A | G |
|
chr9:104902020
|
c.66+1594G>A | Metabolic syndrome0.1 | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Genome-wide screen for metabolic syndrome suscepti others(136): Show |
2,637 European ancestry cases, 7,927 European ance others(14): Show |
ABCA1 | ABCA1 | rs1883025-T | - | MODIFIER | chr9 | C | T |
|
chr9:104891145
|
c.67-1950C>T | HDL cholesterol0.0217 | a0001a0002a0003a0004a0005others(10): Show | a0001c0001a0001c0005a0001c0092a0002c0011a0002c0037others(19): Show | a0001c0001t0006a0001c0001t0011a0001c0001t0012a0001c0001t0049a0001c0005t0010others(37): Show | a0001c0001t0006g0047a0001c0001t0006g0058a0001c0001t0006g0214a0001c0001t0006g0225a0001c0001t0006g0239others(45): Show | HG00423.hp1 HG00423.hp2 HG00544.hp1 HG00558.hp1 HG00621.hp2 others(45): Show |
Large-scale genome-wide association studies in Eas others(64): Show |
12,545 Korean ancestry individuals/Up to 30,395 Ea others(29): Show |
ABCA1 | ABCA1 | rs12686004-T | - | MODIFIER | chr9 | G | A |
|
chr9:104903458
|
c.66+156C>T | Lipid metabolism phenotypes0.14 | a0001a0002a0003a0004a0005others(16): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(42): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0011others(72): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0054others(88): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(88): Show |
Genome-wide association study identifies multiple others(47): Show |
8,330 European ancestry individuals/ | ABCA1 | ABCA1 | rs2575876-? | - | MODIFIER | chr9 | G | A |
|
chr9:104902020
|
c.66+1594G>A | High density lipoprotein cholesterol levelsothers(7): Show | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Genetic analysis of quantitative traits in the Jap others(60): Show |
70,657 Japanese ancestry individuals/ | ABCA1 | ABCA1 | rs1883025-? | - | MODIFIER | chr9 | C | T |
|
chr9:104800276
|
c.4773+234C>T | High density lipoprotein cholesterol levelsothers(8): Show | a0001a0003a0006a0009a0010others(9): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0001c0097others(29): Show | a0001c0001t0001a0001c0001t0002a0001c0001t0003a0001c0001t0004a0001c0001t0006others(76): Show | a0001c0001t0001g0016a0001c0001t0001g0026a0001c0001t0001g0077a0001c0001t0001g0082a0001c0001t0001g0088others(142): Show | HG00099.hp1 HG00099.hp2 HG00408.hp1 HG00423.hp2 HG00544.hp1 others(142): Show |
Genetic analysis of quantitative traits in the Jap others(60): Show |
70,657 Japanese ancestry individuals/ | NR | ABCA1 | rs2740480-? | - | MODIFIER | chr9 | G | A |
|
chr9:104826853
|
c.2337+95T>A | High density lipoprotein cholesterol levelsothers(8): Show | a0002a0003a0004a0005a0006others(21): Show | a0002c0011a0002c0015a0002c0017a0002c0024a0002c0025others(69): Show | a0002c0011t0004a0002c0011t0007a0002c0011t0012a0002c0011t0020a0002c0015t0002others(133): Show | a0002c0011t0004g0112a0002c0011t0004g0213a0002c0011t0004g0263a0002c0011t0007g0119a0002c0011t0007g0247others(186): Show | HG00099.hp2 HG00408.hp2 HG00423.hp2 HG00558.hp1 HG00558.hp2 others(186): Show |
Genetic analysis of quantitative traits in the Jap others(60): Show |
70,657 Japanese ancestry individuals/ | NR | ABCA1 | rs4149310-? | - | MODIFIER | chr9 | A | T |
|
chr9:104902020
|
c.66+1594G>A | HDL cholesterol0.03 | a0001a0002a0003a0004a0005others(20): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(61): Show | a0001c0001t0001a0001c0001t0003a0001c0001t0004a0001c0001t0006a0001c0001t0012others(92): Show | a0001c0001t0001g0082a0001c0001t0003g0211a0001c0001t0004g0021a0001c0001t0006g0047a0001c0001t0006g0058others(111): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00642.hp1 others(111): Show |
Contribution of Rare and Common Genetic Variants t others(102): Show |
3,681 individuals/ | ABCA1 | ABCA1 | rs1883025-A | - | MODIFIER | chr9 | C | T |
|
chr9:104903697
|
c.-18G>C | Waist-hip ratio0.0201 | a0001a0002a0003a0004a0005others(10): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(20): Show | a0001c0001t0006a0001c0001t0011a0001c0001t0012a0001c0001t0049a0001c0005t0010others(36): Show | a0001c0001t0006g0047a0001c0001t0006g0054a0001c0001t0006g0058a0001c0001t0006g0214a0001c0001t0006g0225others(48): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00673.hp1 others(48): Show |
Meta-analysis of genome-wide association studies f others(69): Show |
697,734 European ancestry individuals/ | ABCA1 | rs1800978-C | - | MODIFIER | chr9 | C | G | |
|
chr9:104903697
|
c.-18G>C |
Waist-to-hip ratio adjusted for BMI0.026 others(1): Show |
a0001a0002a0003a0004a0005others(10): Show | a0001c0001a0001c0005a0001c0035a0001c0092a0002c0011others(20): Show | a0001c0001t0006a0001c0001t0011a0001c0001t0012a0001c0001t0049a0001c0005t0010others(36): Show | a0001c0001t0006g0047a0001c0001t0006g0054a0001c0001t0006g0058a0001c0001t0006g0214a0001c0001t0006g0225others(48): Show | HG00423.hp1 HG00544.hp1 HG00558.hp1 HG00621.hp2 HG00673.hp1 others(48): Show |
Meta-analysis of genome-wide association studies f others(69): Show |
379,501 European ancestry female individuals/ | NR | ABCA1 | rs1800978-C | - | MODIFIER | chr9 | C | G |
|
chr9:104924542
|
c.-93+3393C>T |
Waist-to-hip ratio adjusted for BMI0.027 others(1): Show |
a0001a0002a0003a0004a0005others(19): Show | a0001c0001a0001c0005a0001c0035a0002c0011a0002c0015others(55): Show |