Variant report

Variant	rs17100308
Chromosome Location	chr1:77780550-77780551
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1010195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10493604	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11162333	0.83[JPT][hapmap]
rs12133318	0.81[JPT][hapmap]
rs12144794	0.81[JPT][hapmap]
rs12404374	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1377732	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1377735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17100429	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17100475	0.90[JPT][hapmap]
rs2272161	0.86[ASN][1000 genomes]
rs2815321	0.80[ASN][1000 genomes]
rs2815322	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34422174	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3862894	0.85[JPT][hapmap]
rs3921995	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59559185	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72641172	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72641173	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72641174	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72641175	0.86[ASN][1000 genomes]
rs72641176	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs940283	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3452343	chr1:77774348-77781734	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3452344	chr1:77774348-77781734	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3692769	chr1:77774413-77781567	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv11859	chr1:77774744-77781454	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2756848	chr1:77775014-77788462	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv2758945	chr1:77775014-77788462	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77749400-77781600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:77754400-77785800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:77755200-77781600	Weak transcription	Osteobl	bone
4	chr1:77755800-77788200	Weak transcription	HSMMtube	muscle
5	chr1:77756800-77781600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:77759000-77781600	Weak transcription	NHLF	lung
7	chr1:77774000-77790400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:77774800-77787200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:77777000-77794600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:77778000-77781600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:77778800-77783200	Weak transcription	Primary T cells from cord blood	blood
12	chr1:77779200-77784600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:77779400-77794400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:77779600-77781600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:77779600-77781600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:77779600-77781600	Weak transcription	NHEK	skin
17	chr1:77779600-77786200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:77779600-77787200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:77779600-77794600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:77779800-77781400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:77779800-77781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:77780000-77781400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:77780200-77781400	Weak transcription	HSMM	muscle
24	chr1:77780200-77781400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links