JoGo LogoJoint Open Genome and Omics Platform (JoGo)
  • Home
    • General
    • Gene
    • Region
    • Variant
    • Haplotype
    • Haplotype by sample
    • ClinVar
    • GWASCatalog
    • GTEx
    • HaplotypeQTL
    • Haplotype
    • Position
    • Clinvar
    • Gene
    • Variant
    • Haplotype
    • Sample
    • FAQ
    • Contact
    • Fundings
    • Developer
    • ChIP-Atlas PeakBrowser
    • ToGoVAR
    • MGeND
    • Nagasaki Lab

ALDH2_chr12_111761933_111822532 / BRCA1_chr17_43039295_43130364 etc.

  Error connecting to IGV?   TNFRSF6B_chr20_63691652_63703684  TNFRSF6B_chr20_63691652_63703684 (clean+top1000)

Multiple Alignments (by translate haplotype frequency)Multiple Alignments (by aa haplotype frequency) Multiple Alignments (by translate haplotype similarity)Multiple Alignments (by aa haplotype similarity)

Item Value
geneid 8771
ensemblid ENSG00000243509.6
hgncid 11921
symbol TNFRSF6B
name TNF receptor superfamily member 6b
refseq_nuc NM_003823.4
refseq_prot NP_003814.1
ensembl_nuc ENST00000369996.3
ensembl_prot ENSP00000359013.1
mane_status MANE Select
chr chr20
start 63696652
end 63698684
strand +
ver v1.2
region chr20:63696652-63698684
region5000 chr20:63691652-63703684
regionname0 TNFRSF6B_chr20_63696652_63698684
regionname5000 TNFRSF6B_chr20_63691652_63703684

ahapid grch38/
chm13v2 		alen total AFR AMR EAS EUR SAS JPT regionname genename aa chr start end
a0001 1/0 300 30 14 7 2 2 4 2 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0002 0/0 300 2 2 0 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0003 0/0 300 1 0 1 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684

chapid grch38/
chm13v2 		alen clen total AFR AMR EAS EUR SAS regionname genename cseq chr start end
c0001 0/0 903 28 14 7 1 2 4 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
c0002 0/0 903 2 2 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
c0003 1/0 903 1 0 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
c0004 0/0 903 1 0 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
c0005 0/0 903 1 0 0 1 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684

thapid grch38
chm13v2 		tlen total AFR AMR EAS EUR SAS regionname genename tseq chr start end
t0001 1/0 238 29 13 7 2 2 4 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
t0002 0/0 237 4 3 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684

ghapid grch38/
chm13v2 		total AFR AMR EAS EUR SAS regionname genename chr start end
g0001 0/0 23 11 7 1 1 3 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0002 0/0 3 3 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0003 0/0 2 1 0 0 1 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0004 1/0 2 1 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0005 0/0 1 0 0 1 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0006 0/0 1 0 0 0 0 1 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
g0007 0/0 1 0 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684

achapid grch38/
chm13v2 		alen clen total AFR AMR EAS EUR SAS regionname genename cseq chr start end
a0001c0001 0/0 903 28 14 7 1 2 4 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0001c0003 1/0 903 1 0 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0001c0005 0/0 903 1 0 0 1 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0002c0002 0/0 903 2 2 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0003c0004 0/0 903 1 0 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684

acthapid grch38
chm13v2 		tlen total AFR AMR EAS EUR SAS regionname genename tseq chr start end
a0001c0001t0001 0/0 1140 27 13 7 1 2 4 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0001c0001t0002 0/0 1139 1 1 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0001c0003t0001 1/0 1140 1 0 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0001c0005t0001 0/0 1140 1 0 0 1 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0002c0002t0002 0/0 1139 2 2 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684
a0003c0004t0002 0/0 1139 1 0 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B copy fasta chr20 63691652 63703684

actghapid grch38/
chm13v2 		total AFR AMR EAS EUR SAS regionname genename chr start end
a0001c0001t0001g0001 0/0 23 11 7 1 1 3 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0001t0001g0003 0/0 2 1 0 0 1 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0001t0001g0004 0/0 1 1 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0001t0001g0006 0/0 1 0 0 0 0 1 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0001t0002g0002 0/0 1 1 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0003t0001g0004 1/0 1 0 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0001c0005t0001g0005 0/0 1 0 0 1 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0002c0002t0002g0002 0/0 2 2 0 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
a0003c0004t0002g0007 0/0 1 0 1 0 0 0 TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684

sampleid ID
haplotypeid
 ahapid chapid thapid ghapid gpopname popname regionname genename chr start end
HG00642 hp1 a0001 c0001 t0001 g0001 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG00642 hp2 a0001 c0001 t0001 g0001 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01106 hp1 a0001 c0001 t0001 g0001 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01106 hp2 a0001 c0001 t0001 g0001 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01167 hp1 a0003 c0004 t0002 g0007 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01167 hp2 a0001 c0001 t0001 g0001 AMR PUR TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01361 hp1 a0001 c0001 t0001 g0001 AMR CLM TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG01361 hp2 a0001 c0001 t0001 g0001 AMR CLM TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02451 hp1 a0001 c0001 t0001 g0001 AFR ACB TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02451 hp2 a0001 c0001 t0001 g0001 AFR ACB TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02622 hp1 a0001 c0001 t0001 g0001 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02622 hp2 a0001 c0001 t0001 g0001 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02630 hp1 a0002 c0002 t0002 g0002 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02630 hp2 a0001 c0001 t0001 g0001 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02886 hp1 a0001 c0001 t0001 g0001 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02886 hp2 a0001 c0001 t0001 g0001 AFR GWD TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02922 hp1 a0001 c0001 t0001 g0001 AFR ESN TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG02922 hp2 a0001 c0001 t0001 g0001 AFR ESN TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03139 hp1 a0001 c0001 t0001 g0004 AFR ESN TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03139 hp2 a0001 c0001 t0002 g0002 AFR ESN TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03239 hp1 a0001 c0001 t0001 g0001 SAS PJL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03239 hp2 a0001 c0001 t0001 g0001 SAS PJL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03669 hp1 a0001 c0001 t0001 g0001 SAS PJL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03669 hp2 a0001 c0001 t0001 g0006 SAS PJL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA18906 hp1 a0002 c0002 t0002 g0002 AFR YRI TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA18906 hp2 a0001 c0001 t0001 g0003 AFR YRI TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA18993 hp1 a0001 c0005 t0001 g0005 EAS JPT TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA18993 hp2 a0001 c0001 t0001 g0001 EAS JPT TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA20752 hp1 a0001 c0001 t0001 g0003 EUR TSI TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
NA20752 hp2 a0001 c0001 t0001 g0001 EUR TSI TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03471 hp1 a0001 c0001 t0001 g0001 AFR MSL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
HG03471 hp2 a0001 c0001 t0001 g0001 AFR MSL TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684
homoSapiens_grch38 hp1 a0001 c0003 t0001 g0004 REF REF TNFRSF6B_chr20_63691652_63703684 TNFRSF6B chr20 63691652 63703684

chr:pos ref alt #
# of ahapid:amino-acid(protein) level
 ahapids #
# of haplotypeids
 haplotypeids annotation impact hgvs_c hgvs_p genename geneid featuretype featureid transcript_biotype rank cdna
cdna pos length
 cds
cds pos length
 aa
aa pos length
 distance status chr pos
chr20:63696883 G
G
 A
A
 1 a0002
a0002
 2 HG02630.hp1
NA18906.hp1
HG02630.hp1
NA18906.hp1
 missense_variant MODERATE c.116G>A
c.116G>A
 p.Arg39Gln
p.Arg39Gln
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 1/3 232/1140 116/903 39/300 chr20 63696883
chr20:63698538 G
G
 A
A
 1 a0003
a0003
 1 HG01167.hp1
HG01167.hp1
 missense_variant MODERATE c.878G>A
c.878G>A
 p.Arg293His
p.Arg293His
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 3/3 994/1140 878/903 293/300 chr20 63698538

chr:pos ref alt #
# of chapid
 chapids #
# of haplotypeids
 haplotypeids annotation impact hgvs_c hgvs_p genename geneid featuretype featureid transcript_biotype rank cdna
cdna pos length
 cds
cds pos length
 aa
aa pos length
 distance status chr pos
chr20:63696914 C
C
 T
T
 1 a0001c0005
a0001c0005
 1 NA18993.hp1
NA18993.hp1
 synonymous_variant LOW c.147C>T
c.147C>T
 p.Cys49Cys
p.Cys49Cys
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 1/3 263/1140 147/903 49/300 chr20 63696914
chr20:63697022 A
A
 G
G
 4 a0001c0001
a0001c0005
a0002c0002
others(1): Show 
a0001c0001
a0001c0005
a0002c0002
a0003c0004
 32 HG00642.hp1
HG00642.hp2
HG01106.hp1
others(29): Show 
HG00642.hp1
HG00642.hp2
HG01106.hp1
HG01106.hp2
HG01167.hp1
HG01167.hp2
HG01361.hp1
HG01361.hp2
HG02451.hp1
HG02451.hp2
HG02622.hp1
HG02622.hp2
HG02630.hp1
HG02630.hp2
HG02886.hp1
HG02886.hp2
HG02922.hp1
HG02922.hp2
HG03139.hp1
HG03139.hp2
HG03239.hp1
HG03239.hp2
HG03471.hp1
HG03471.hp2
HG03669.hp1
HG03669.hp2
NA18906.hp1
NA18906.hp2
NA18993.hp1
NA18993.hp2
NA20752.hp1
NA20752.hp2
 synonymous_variant LOW c.255A>G
c.255A>G
 p.Leu85Leu
p.Leu85Leu
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 1/3 371/1140 255/903 85/300 chr20 63697022
chr20:63697100 T
T
 C
C
 1 a0001c0005
a0001c0005
 1 NA18993.hp1
NA18993.hp1
 synonymous_variant LOW c.333T>C
c.333T>C
 p.Arg111Arg
p.Arg111Arg
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 1/3 449/1140 333/903 111/300 chr20 63697100
chr20:63697389 C
C
 T
T
 1 a0001c0005
a0001c0005
 1 NA18993.hp1
NA18993.hp1
 synonymous_variant LOW c.486C>T
c.486C>T
 p.Ser162Ser
p.Ser162Ser
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/3 602/1140 486/903 162/300 chr20 63697389
chr20:63697476 C
C
 G
G
 1 a0001c0005
a0001c0005
 1 NA18993.hp1
NA18993.hp1
 synonymous_variant LOW c.573C>G
c.573C>G
 p.Thr191Thr
p.Thr191Thr
 TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/3 689/1140 573/903 191/300 chr20 63697476

chr:pos ref alt #
# of thapid:transcript level
 thapids #
# of haplotypeids
 haplotypeids annotation impact hgvs_c hgvs_p genename geneid featuretype featureid transcript_biotype rank cdna
cdna pos length
 cds
cds pos length
 aa
aa pos length
 distance status chr pos
chr20:63698660 AT
AT
 A
A
 3 a0001c0001t0002
a0002c0002t0002
a0003c0004t0002
a0001c0001t0002
a0002c0002t0002
a0003c0004t0002
 4 HG01167.hp1
HG02630.hp1
HG03139.hp2
others(1): Show 
HG01167.hp1
HG02630.hp1
HG03139.hp2
NA18906.hp1
 3_prime_UTR_variant MODIFIER c.*102delT
c.*102delT
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 3/3 102 INFO_REALIGN_3_PRIME chr20 63698660

chr:pos ref alt #
# of ghapid:genebody level
 ghapids #
# of haplotypeids
 haplotypeids annotation impact hgvs_c hgvs_p genename geneid featuretype featureid genebody_biotype rank cdna
cdna pos length
 cds
cds pos length
 aa
aa pos length
 distance status chr pos
chr20:63697587 C
C
 T
T
 3 a0001c0001t0002g0002
a0002c0002t0002g0002
a0003c0004t0002g0007
a0001c0001t0002g0002
a0002c0002t0002g0002
a0003c0004t0002g0007
 4 HG01167.hp1
HG02630.hp1
HG03139.hp2
others(1): Show 
HG01167.hp1
HG02630.hp1
HG03139.hp2
NA18906.hp1
 intron_variant MODIFIER c.619+65C>T
c.619+65C>T
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63697587
chr20:63697665 C
C
 T
T
 1 a0001c0001t0001g0006
a0001c0001t0001g0006
 1 HG03669.hp2
HG03669.hp2
 intron_variant MODIFIER c.619+143C>T
c.619+143C>T
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63697665
chr20:63697746 G
G
 A
A
 2 a0001c0001t0001g0001
a0001c0001t0001g0003
a0001c0001t0001g0001
a0001c0001t0001g0003
 25 HG00642.hp1
HG00642.hp2
HG01106.hp1
others(22): Show 
HG00642.hp1
HG00642.hp2
HG01106.hp1
HG01106.hp2
HG01167.hp2
HG01361.hp1
HG01361.hp2
HG02451.hp1
HG02451.hp2
HG02622.hp1
HG02622.hp2
HG02630.hp2
HG02886.hp1
HG02886.hp2
HG02922.hp1
HG02922.hp2
HG03239.hp1
HG03239.hp2
HG03471.hp1
HG03471.hp2
HG03669.hp1
NA18906.hp2
NA18993.hp2
NA20752.hp1
NA20752.hp2
 intron_variant MODIFIER c.619+224G>A
c.619+224G>A
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63697746
chr20:63697813 C
C
 T
T
 1 a0001c0001t0001g0003
a0001c0001t0001g0003
 2 NA18906.hp2
NA20752.hp1
NA18906.hp2
NA20752.hp1
 intron_variant MODIFIER c.619+291C>T
c.619+291C>T
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63697813
chr20:63697816 G
G
 A
A
 1 a0001c0005t0001g0005
a0001c0005t0001g0005
 1 NA18993.hp1
NA18993.hp1
 intron_variant MODIFIER c.619+294G>A
c.619+294G>A
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63697816
chr20:63698059 G
G
 A
A
 1 a0001c0005t0001g0005
a0001c0005t0001g0005
 1 NA18993.hp1
NA18993.hp1
 intron_variant MODIFIER c.620-221G>A
c.620-221G>A
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63698059
chr20:63698114 C
C
 T
T
 1 a0003c0004t0002g0007
a0003c0004t0002g0007
 1 HG01167.hp1
HG01167.hp1
 intron_variant MODIFIER c.620-166C>T
c.620-166C>T
TNFRSF6B ENSG00000243509.6 transcript ENST00000369996.3 protein_coding 2/2 chr20 63698114

  • GeneCards
  • OpenTarget
  • The Human Protein Atlas
  • Gnomad v4.1.0
  • PhewebJP (Japan)
  • UKB-TOPMed (UMich) (UK and US)
  • FinnGen r11 (Finland)
  • KoGES (Korean)
  • Mouse Phenotype
  • Zebra Phenotype
  • TogoVar

  • DNA
  • Satellite
  • All Snps 1.4.2
  • RC
  • snRNA
  • SINE
  • GC %
  • Simple_repeat
  • RNA
  • Retroposon
  • Unknown
  • Low_complexity
  • LINE
  • scRNA
  • CpG Islands
  • Phastcons (20 way)
  • srpRNA
  • Common Snps 1.4.2
  • rRNA
  • LTR
  • tRNA

  • Axiom Genome-Wide Array (Japonica Array V1)
  • Axiom Genome-Wide Array (Japonica Array V2)
  • Axiom Genome-Wide ASI Array V1 (ASI V1)
​

IGV Connection Help

IGV must be running on your computer before clicking the button.

If your browser shows the "cannot open the page" error, launch IGV and allow access via port 60151:

  1. Open IGV on your computer
  2. In IGV's menu bar: View → Preferences…
  3. Click on the "Advanced" tab
  4. Check "Enable port"
  5. Set the port number to 60151
  6. Click OK to save

For more details, please refer to Information → FAQ.