Variant report

Variant	rs17401994
Chromosome Location	chr1:79298460-79298461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10518590	0.85[EUR][1000 genomes]
rs17102289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102309	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102367	0.85[EUR][1000 genomes]
rs2996692	1.00[EUR][1000 genomes]
rs41312730	0.80[EUR][1000 genomes]
rs57388815	1.00[EUR][1000 genomes]
rs6424614	0.95[EUR][1000 genomes]
rs6667376	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6682731	1.00[EUR][1000 genomes]
rs6690213	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7516845	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7525345	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7528069	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7531816	0.97[EUR][1000 genomes]
rs7535891	1.00[EUR][1000 genomes]
rs7543576	1.00[EUR][1000 genomes]
rs7543883	1.00[EUR][1000 genomes]
rs7549910	1.00[EUR][1000 genomes]
rs984361	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs984656	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999624	chr1:79230028-79448222	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535013	chr1:79230028-79448222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546619	chr1:79233493-79614989	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17401994	TBX1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79295800-79300000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:79296000-79299200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:79296000-79299800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:79296000-79300000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:79296000-79300200	Enhancers	NH-A	brain
6	chr1:79296000-79300200	Enhancers	NHDF-Ad	bronchial
7	chr1:79296000-79300200	Enhancers	Osteobl	bone
8	chr1:79296800-79300200	Enhancers	HMEC	breast
9	chr1:79297000-79299600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:79297000-79300400	Enhancers	HSMM	muscle
11	chr1:79297000-79300400	Enhancers	HUVEC	blood vessel
12	chr1:79297200-79299800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:79297400-79299000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:79297400-79299400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:79297400-79299600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:79297600-79299800	Enhancers	Hela-S3	cervix
17	chr1:79297800-79299800	Enhancers	NHEK	skin
18	chr1:79298000-79299000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:79298000-79299200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:79298000-79299800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:79298000-79300000	Enhancers	NHLF	lung
22	chr1:79298200-79298600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:79298200-79298600	Enhancers	HSMMtube	muscle

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