Variant report

Variant	rs4916390
Chromosome Location	chr1:171097561-171097562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10797877	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911192	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911839	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10911841	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11811455	0.90[ASN][1000 genomes]
rs12076145	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16864096	0.90[ASN][1000 genomes]
rs1736564	0.81[EUR][1000 genomes]
rs1736565	0.81[EUR][1000 genomes]
rs1795240	0.82[EUR][1000 genomes]
rs1795241	0.81[EUR][1000 genomes]
rs1920137	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1920144	0.88[ASN][1000 genomes]
rs1920149	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920151	0.90[ASN][1000 genomes]
rs1920152	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1920153	0.90[ASN][1000 genomes]
rs1920154	0.90[ASN][1000 genomes]
rs2064074	0.85[EUR][1000 genomes]
rs2064076	0.87[EUR][1000 genomes]
rs2064079	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2064080	0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2235193	0.88[ASN][1000 genomes]
rs2281003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67727346	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7886526	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4916390	SCYL3	cis	parietal	SCAN
rs4916390	C1orf156	cis	parietal	SCAN
rs4916390	XCL1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171091000-171098200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:171091600-171109000	Weak transcription	Right Ventricle	heart
3	chr1:171095800-171097600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:171095800-171098000	Enhancers	NHLF	lung
5	chr1:171096000-171097600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:171096000-171097600	Enhancers	NH-A	brain
7	chr1:171096200-171097800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:171096200-171098000	Enhancers	Osteobl	bone
9	chr1:171096600-171098000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:171096600-171098000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:171097000-171098000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:171097200-171097600	Enhancers	Aorta	Aorta
13	chr1:171097200-171097600	ZNF genes & repeats	Lung	lung
14	chr1:171097200-171097800	Enhancers	Esophagus	oesophagus
15	chr1:171097200-171097800	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr1:171097200-171097800	Enhancers	Gastric	stomach
17	chr1:171097200-171097800	Enhancers	Left Ventricle	heart
18	chr1:171097200-171097800	Enhancers	Ovary	ovary
19	chr1:171097200-171098800	Weak transcription	Fetal Lung	lung
20	chr1:171097400-171098000	ZNF genes & repeats	Pancreas	Pancrea

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