Variant report

Variant	rs1693457
Chromosome Location	chr4:100236762-100236763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002894	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10008281	0.87[YRI][hapmap]
rs1229967	0.85[ASN][1000 genomes]
rs1229969	0.85[ASN][1000 genomes]
rs1229970	0.85[ASN][1000 genomes]
rs1229976	0.85[ASN][1000 genomes]
rs1229977	0.85[ASN][1000 genomes]
rs1229982	1.00[CHB][hapmap]
rs1230019	0.85[ASN][1000 genomes]
rs1230020	0.85[ASN][1000 genomes]
rs1230022	0.85[ASN][1000 genomes]
rs1230025	0.85[ASN][1000 genomes]
rs1230026	0.85[ASN][1000 genomes]
rs1230027	0.85[ASN][1000 genomes]
rs1230028	0.85[ASN][1000 genomes]
rs1497375	0.85[ASN][1000 genomes]
rs1587264	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1618572	0.85[ASN][1000 genomes]
rs1693458	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789882	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066702	0.82[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2173200	0.85[ASN][1000 genomes]
rs2646009	0.85[ASN][1000 genomes]
rs2646011	0.85[ASN][1000 genomes]
rs2851291	0.85[ASN][1000 genomes]
rs28600890	0.85[AFR][1000 genomes]
rs2866149	0.85[ASN][1000 genomes]
rs28864441	0.87[AFR][1000 genomes]
rs3133155	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4355398	0.85[ASN][1000 genomes]
rs4699733	0.82[JPT][hapmap]
rs4699737	0.81[ASN][1000 genomes]
rs62305755	0.85[ASN][1000 genomes]
rs6532810	0.85[ASN][1000 genomes]
rs6532811	0.85[ASN][1000 genomes]
rs6532813	0.85[ASN][1000 genomes]
rs6830685	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs7656223	0.85[ASN][1000 genomes]
rs7669784	0.85[ASN][1000 genomes]
rs7673231	0.85[ASN][1000 genomes]
rs7684914	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs904092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931635	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9995799	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3446139	chr4:100213459-100244162	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3387812	chr4:100232775-100261923	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv966300	chr4:100233771-100237318	Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1002809	chr4:100234048-100285508	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1693457	ADH1A	cis	Adipose Subcutaneous	GTEx
rs1693457	ADH1A	cis	lung	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100223200-100237000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:100231000-100238600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:100231000-100243000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:100231200-100242800	Weak transcription	Gastric	stomach
5	chr4:100232800-100237000	Weak transcription	Aorta	Aorta
6	chr4:100233000-100244400	Weak transcription	NHDF-Ad	bronchial
7	chr4:100233400-100237000	Genic enhancers	Adipose Nuclei	Adipose
8	chr4:100233600-100239600	Weak transcription	Esophagus	oesophagus
9	chr4:100234000-100238600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:100234000-100238600	Weak transcription	Lung	lung
11	chr4:100235000-100237600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:100235400-100237000	Strong transcription	Ovary	ovary
13	chr4:100235600-100238600	Genic enhancers	Liver	Liver
14	chr4:100235600-100238600	Weak transcription	Small Intestine	intestine
15	chr4:100236200-100237000	Genic enhancers	Fetal Lung	lung
16	chr4:100236200-100238600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:100236600-100238400	Weak transcription	Right Atrium	heart

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