Variant report

Variant	rs1990618
Chromosome Location	chr2:40852952-40852953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1003618	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177056	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178374	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178666	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180556	0.91[EUR][1000 genomes]
rs10469903	0.85[ASN][1000 genomes]
rs10469904	0.85[ASN][1000 genomes]
rs11124758	0.91[EUR][1000 genomes]
rs12475258	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478853	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12619861	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016243	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379037	0.85[ASN][1000 genomes]
rs1456578	0.85[ASN][1000 genomes]
rs1456581	0.85[ASN][1000 genomes]
rs1456582	0.85[ASN][1000 genomes]
rs1456583	0.85[ASN][1000 genomes]
rs1456588	0.92[ASN][1000 genomes]
rs1468799	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173799	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs173802	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173803	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173805	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1840756	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1861308	0.94[EUR][1000 genomes]
rs2019379	0.85[ASN][1000 genomes]
rs2019768	0.94[EUR][1000 genomes]
rs2192821	0.94[EUR][1000 genomes]
rs2216035	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373898	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373904	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2373936	0.91[EUR][1000 genomes]
rs3922281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42784	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4539838	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952636	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952642	0.94[EUR][1000 genomes]
rs6544354	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6709044	0.91[EUR][1000 genomes]
rs6709173	0.91[EUR][1000 genomes]
rs6713163	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728651	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743662	1.00[EUR][1000 genomes]
rs6750481	0.91[EUR][1000 genomes]
rs6753289	0.92[ASN][1000 genomes]
rs67806170	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7369131	0.84[EUR][1000 genomes]
rs7556714	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs756376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564682	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7587020	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7591373	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591414	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7596941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605586	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309059	0.94[EUR][1000 genomes]
rs993867	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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
3	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv873918	chr2:40805427-40890416	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873919	chr2:40815238-40853317	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv470454	chr2:40815238-40896385	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv456429	chr2:40823026-40896385	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv581507	chr2:40823026-40896385	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv581508	chr2:40833142-40890416	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	nsv873920	chr2:40833142-40890416	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	nsv581509	chr2:40835285-40857899	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
13	nsv581510	chr2:40835285-40869165	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	nsv873921	chr2:40835285-40869165	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
15	nsv873922	chr2:40835285-40876113	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
16	nsv873923	chr2:40835285-40890416	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
17	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
18	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv873930	chr2:40837953-40857529	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
25	nsv581511	chr2:40839418-40863036	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
26	nsv581512	chr2:40843613-40869165	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
27	nsv581513	chr2:40843613-40896385	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40844400-40853000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:40852200-40853800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:40852400-40853200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:40852400-40853200	Enhancers	NHDF-Ad	bronchial
5	chr2:40852400-40854000	Enhancers	NHEK	skin
6	chr2:40852600-40853400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:40852600-40853400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:40852800-40853600	Enhancers	Osteobl	bone

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