Variant report

Variant	rs1990617
Chromosome Location	chr2:40853040-40853041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10183264	0.81[EUR][1000 genomes]
rs11124754	0.85[ASN][1000 genomes]
rs11124756	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11491284	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11887013	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11898380	0.81[ASN][1000 genomes]
rs11899009	0.83[ASN][1000 genomes]
rs12469563	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12474948	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12477643	0.81[EUR][1000 genomes]
rs12712704	0.83[ASN][1000 genomes]
rs13386194	0.81[EUR][1000 genomes]
rs13389197	0.81[EUR][1000 genomes]
rs1541575	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17026290	0.81[EUR][1000 genomes]
rs17026319	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17026434	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17026446	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17026480	0.81[EUR][1000 genomes]
rs17026537	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17026541	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17026544	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17026584	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17026612	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17026616	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17026644	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2005413	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2052260	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2110789	0.80[AMR][1000 genomes]
rs2160262	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2888699	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3915716	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs42787	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597578	0.81[EUR][1000 genomes]
rs4610094	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4952643	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952644	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5022306	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55973449	0.81[EUR][1000 genomes]
rs56322026	0.81[EUR][1000 genomes]
rs56407568	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57225071	0.81[EUR][1000 genomes]
rs57569001	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57770208	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57955071	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57988012	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59892061	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60373384	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61275311	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544345	0.84[ASN][1000 genomes]
rs72945712	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7369946	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7369960	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7423585	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7581499	0.81[EUR][1000 genomes]
rs7608684	0.83[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	chr2:40852200-40853800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:40852400-40853200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:40852400-40853200	Enhancers	NHDF-Ad	bronchial
4	chr2:40852400-40854000	Enhancers	NHEK	skin
5	chr2:40852600-40853400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:40852600-40853400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:40852800-40853600	Enhancers	Osteobl	bone
8	chr2:40853000-40854200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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