| geneid | 675 |
|---|---|
| ensemblid | ENSG00000139618.18 |
| hgncid | 1101 |
| symbol | BRCA2 |
| name | BRCA2 DNA repair associated |
| refseq_nuc | NM_000059.4 |
| refseq_prot | NP_000050.3 |
| ensembl_nuc | ENST00000380152.8 |
| ensembl_prot | ENSP00000369497.3 |
| mane_status | MANE Select |
| chr | chr13 |
| start | 32315508 |
| end | 32400268 |
| strand | + |
| ver | v1.2 |
| region | chr13:32315508-32400268 |
| region5000 | chr13:32310508-32405268 |
| regionname0 | BRCA2_chr13_32315508_32400268 |
| regionname5000 | BRCA2_chr13_32310508_32405268 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr13:32332592
|
A | C | 0.2111 | missense_variant | MODERATE | HG00099.hp1 HG00280.hp2 HG00323.hp1 others(81): Show |
a0002a0008a0009others(4): Show | a0002c0002a0002c0048a0008c0013others(5): Show | a0002c0002t0002a0002c0002t0004a0002c0002t0006others(14): Show | a0002c0002t0002g0004a0002c0002t0002g0005a0002c0002t0002g0012others(74): Show | 84 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 10/27 | c.1114A>C | p.Asn372His | 1313/11954 | 1114/10257 | 372/3418 | ||
|
chr13:32340486
|
G | T | 0.0025 | missense_variant | MODERATE | NA18965.hp2 | a0019 | a0019c0047 | a0019c0047t0002 | a0019c0047t0002g0180 | 1 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 11/27 | c.6131G>T | p.Gly2044Val | 6330/11954 | 6131/10257 | 2044/3418 | ||
|
chr13:32355250
|
T | C | 0.9774 | missense_variant | MODERATE | HG00099.hp1 HG00099.hp2 HG00280.hp1 others(386): Show |
a0001a0002a0003others(34): Show | a0001c0001a0001c0003a0001c0004others(45): Show | a0001c0001t0001a0001c0001t0008a0001c0001t0009others(81): Show | a0001c0001t0001g0001a0001c0001t0001g0003a0001c0001t0001g0015others(365): Show | 389 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 14/27 | c.7397T>C | p.Val2466Ala | 7596/11954 | 7397/10257 | 2466/3418 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr13:32338918
|
A | G | 0.9774 | synonymous_variant | LOW | HG00099.hp1 HG00099.hp2 HG00280.hp1 others(386): Show |
a0001a0002a0003others(35): Show | a0001c0001a0001c0003a0001c0004others(45): Show | a0001c0001t0001a0001c0001t0008a0001c0001t0009others(81): Show | a0001c0001t0001g0001a0001c0001t0001g0003a0001c0001t0001g0015others(365): Show | 389 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 11/27 | c.4563A>G | p.Leu1521Leu | 4762/11954 | 4563/10257 | 1521/3418 | ||
|
chr13:32340868
|
G | C | 0.9749 | synonymous_variant | LOW | HG00099.hp1 HG00099.hp2 HG00280.hp1 others(385): Show |
a0001a0002a0003others(34): Show | a0001c0001a0001c0003a0001c0004others(44): Show | a0001c0001t0001a0001c0001t0008a0001c0001t0009others(80): Show | a0001c0001t0001g0001a0001c0001t0001g0003a0001c0001t0001g0015others(364): Show | 388 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 11/27 | c.6513G>C | p.Val2171Val | 6712/11954 | 6513/10257 | 2171/3418 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr13:32399885
|
C | A | 0.9975 | 3_prime_UTR_variant | MODIFIER | HG00099.hp1 HG00099.hp2 HG00280.hp1 others(394): Show |
a0001a0002a0003others(35): Show | a0001c0001a0001c0003a0001c0004others(48): Show | a0001c0001t0001a0001c0001t0008a0001c0001t0009others(85): Show | a0001c0001t0001g0001a0001c0001t0001g0003a0001c0001t0001g0015others(373): Show | 397 | 398 | 0 | BRCA2 | ENSG00000139618.18 | transcript | ENST00000380152.8 | protein_coding | 27/27 | c.*1115C>A | 1115 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | 0/0 | a0019 | 3418 | 1 | 0 | 0 | 1 | 0 | 0 | subcellular location copy fasta | chr13 | 32310508 | 32405268 |
| 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
|
chapid | clen | total | AFR | AMR | EAS | EUR | SAS | cseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | 0/0 | c0047 | 10257 | 1 | 0 | 0 | 1 | 0 | 0 | copy fasta | chr13 | 32310508 | 32405268 |
| genename | grch38/chm13v2 | thapid | tlen | total | AFR | AMR | EAS | EUR | SAS | tseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | 0/1 | t0002 | 1698 | 59 | 3 | 12 | 35 | 2 | 6 | copy fasta | chr13 | 32310508 | 32405268 |
| 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 |
achapid | total | AFR | AMR | EAS | EUR | SAS | clen | cseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | 0/0 | a0019c0047 | 1 | 0 | 0 | 1 | 0 | 0 | 10257 | copy fasta | chr13 | 32310508 | 32405268 |
| 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 |
acthapid | total | AFR | AMR | EAS | EUR | SAS | tlen | tseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | 0/0 | a0019c0047t0002 | 1 | 0 | 0 | 1 | 0 | 0 | 11954 | copy fasta | chr13 | 32310508 | 32405268 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 32315667 | + | 1 | -0.5608 | -0.5608 | -0.5608 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32316422 | + | 2 | 0.9503 | 0.9503 | 0.9503 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32316527 | + | 2 | -0.9071 | -0.9071 | -0.9071 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32319077 | + | 3 | 0.9701 | 0.9701 | 0.9701 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32319325 | + | 3 | -0.9600 | -0.9600 | -0.9600 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32325076 | + | 4 | 0.9830 | 0.9830 | 0.9830 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32325184 | + | 4 | -0.9936 | -0.9936 | -0.9936 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326101 | + | 5 | 0.9829 | 0.9829 | 0.9829 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326150 | + | 5 | -0.9822 | -0.9822 | -0.9822 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326242 | + | 6 | 0.9766 | 0.9766 | 0.9766 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326282 | + | 6 | -0.9802 | -0.9802 | -0.9802 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326499 | + | 7 | 0.7783 | 0.7783 | 0.7783 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32326613 | + | 7 | -0.8100 | -0.8100 | -0.8100 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32329443 | + | 8 | 0.9949 | 0.9949 | 0.9949 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32329492 | + | 8 | -0.9956 | -0.9956 | -0.9956 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32330919 | + | 9 | 0.9989 | 0.9989 | 0.9989 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32331030 | + | 9 | -0.9986 | -0.9986 | -0.9986 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32332272 | + | 10 | 0.9952 | 0.9952 | 0.9952 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32333387 | + | 10 | -0.9923 | -0.9923 | -0.9923 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32336265 | + | 11 | 0.9853 | 0.9853 | 0.9853 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32341196 | + | 11 | -0.9511 | -0.9511 | -0.9511 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32344558 | + | 12 | 0.9804 | 0.9804 | 0.9804 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32344653 | + | 12 | -0.9503 | -0.9503 | -0.9503 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32346827 | + | 13 | 0.9964 | 0.9964 | 0.9964 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32346896 | + | 13 | -0.9973 | -0.9973 | -0.9973 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32354861 | + | 14 | 0.9761 | 0.9761 | 0.9761 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32355288 | + | 14 | -0.9943 | -0.9943 | -0.9943 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32356428 | + | 15 | 0.9491 | 0.9491 | 0.9491 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32356609 | + | 15 | -0.9774 | -0.9774 | -0.9774 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32357742 | + | 16 | 0.9945 | 0.9945 | 0.9945 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32357929 | + | 16 | -0.9788 | -0.9788 | -0.9788 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32362523 | + | 17 | 0.9668 | 0.9668 | 0.9668 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32362693 | + | 17 | -0.9291 | -0.9291 | -0.9291 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32363179 | + | 18 | 0.9831 | 0.9831 | 0.9831 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32363533 | + | 18 | -0.9799 | -0.9799 | -0.9799 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32370402 | + | 19 | 0.9887 | 0.9887 | 0.9887 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32370557 | + | 19 | -0.9607 | -0.9607 | -0.9607 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32370956 | + | 20 | 0.9205 | 0.9205 | 0.9205 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32371100 | + | 20 | -0.9857 | -0.9857 | -0.9857 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32376670 | + | 21 | 0.9972 | 0.9972 | 0.9972 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32376791 | + | 21 | -0.9928 | -0.9928 | -0.9928 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32379317 | + | 22 | 0.9896 | 0.9896 | 0.9896 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32379515 | + | 22 | -0.9894 | -0.9894 | -0.9894 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32379750 | + | 23 | 0.8972 | 0.8972 | 0.8972 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32379913 | + | 23 | -0.9330 | -0.9330 | -0.9330 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32380007 | + | 24 | 0.9955 | 0.9955 | 0.9955 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32380145 | + | 24 | -0.9986 | -0.9986 | -0.9986 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32394689 | + | 25 | 0.9970 | 0.9970 | 0.9970 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32394933 | + | 25 | -0.9981 | -0.9981 | -0.9981 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32396898 | + | 26 | 0.9950 | 0.9950 | 0.9950 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32397044 | + | 26 | -0.9974 | -0.9974 | -0.9974 | 0.0000 | acceptor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 32398162 | + | 27 | 0.9569 | 0.9569 | 0.9569 | 0.0000 | donor | a0019c0047t0002 | NA18965.hp2 | NA18965.hp2 | BRCA2 | chr13 | 32310508 | 32405268 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
chr13:32346481
|
c.6938-346G>A | Triglycerides in medium LDL0.0247 | a0001a0002a0004a0008a0009others(8): Show | a0001c0003a0001c0004a0002c0002a0002c0048a0004c0006others(12): Show | a0001c0003t0014a0001c0003t0036a0001c0004t0003a0001c0004t0005a0001c0004t0006others(28): Show | a0001c0003t0014g0078a0001c0003t0014g0079a0001c0003t0014g0080a0001c0003t0036g0081a0001c0004t0003g0345others(136): Show | HG00099.hp1 HG00280.hp1 HG00280.hp2 HG00323.hp1 HG00323.hp2 others(148): Show |
Genome-wide characterization of circulating metabo others(15): Show |
4,435 East Asian ancestry individuals, 11,340 Sout others(68): Show |
BRCA2 | rs206079-A | + | MODIFIER | chr13 | G | A | |
|
chr13:32403395
|
c.*4625C>G | Educational attainment0.00797085 | a0001a0002a0011a0019a0024others(5): Show | a0001c0001a0001c0003a0001c0004a0001c0010a0002c0002others(8): Show | a0001c0001t0001a0001c0001t0017a0001c0003t0004a0001c0003t0010a0001c0003t0021others(15): Show | a0001c0001t0001g0191a0001c0001t0001g0192a0001c0001t0001g0193a0001c0001t0001g0194a0001c0001t0001g0199others(85): Show | HG00280.hp1 HG00558.hp1 HG00597.hp2 HG00609.hp2 HG00621.hp2 others(91): Show |
Polygenic prediction of educational attainment wit others(88): Show |
3,037,499 European ancestry individuals/ | N4BP2L1 | rs1207953-C | + | MODIFIER | chr13 | C | G |