Variant report

Variant	rs12490361
Chromosome Location	chr3:162520560-162520561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 600 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11916098	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11916381	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11916978	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11919987	0.89[EUR][1000 genomes]
rs11923230	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11927742	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12185924	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12185935	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12185939	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12485259	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12487920	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12487950	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12487989	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12488804	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12488906	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12496306	0.87[EUR][1000 genomes]
rs13059885	0.91[EUR][1000 genomes]
rs13062014	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13062186	0.84[EUR][1000 genomes]
rs13064081	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13064229	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13066346	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13066770	0.84[EUR][1000 genomes]
rs13067404	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068477	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13073727	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13074527	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076294	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13082156	0.89[EUR][1000 genomes]
rs13082299	0.89[EUR][1000 genomes]
rs13083125	0.83[EUR][1000 genomes]
rs13084011	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13086592	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13086937	0.86[EUR][1000 genomes]
rs13091715	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13092421	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13097285	0.82[EUR][1000 genomes]
rs13098325	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13098441	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2080523	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2193271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62393499	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:558 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv877758	chr3:162287573-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv877759	chr3:162303276-162521339	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877761	chr3:162346392-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1005637	chr3:162379324-162635451	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv877762	chr3:162400620-162521339	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv869804	chr3:162414099-162776884	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv829776	chr3:162422424-162577578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv999246	chr3:162447248-162625983	Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv592210	chr3:162447818-162633607	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv877763	chr3:162455815-162521339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2757902	chr3:162471049-162742794	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv2759197	chr3:162471049-162742794	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv870377	chr3:162474576-162630179	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv877767	chr3:162474834-162521339	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv4093	chr3:162479653-162654587	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv870072	chr3:162483397-162630179	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv869992	chr3:162483397-162776884	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1010892	chr3:162484827-162540478	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv536781	chr3:162486046-162600545	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv536782	chr3:162486046-162635451	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	nsv877768	chr3:162486664-162521339	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv877769	chr3:162486664-162626585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv877770	chr3:162490482-162626585	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv869653	chr3:162494699-162641112	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
30	nsv870318	chr3:162494699-162819441	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv592211	chr3:162494772-162618885	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv1007442	chr3:162495253-162625983	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv877771	chr3:162498758-162626585	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv536783	chr3:162502851-162635451	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
35	nsv1002011	chr3:162503110-162524846	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv1000138	chr3:162503110-162546217	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv1008829	chr3:162503110-162564043	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv1009948	chr3:162503110-162599175	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv998809	chr3:162503110-162613956	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
40	nsv1008592	chr3:162503110-162615903	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv1014614	chr3:162503110-162623869	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv1014258	chr3:162503110-162623885	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv1010880	chr3:162503110-162625983	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
44	nsv1004966	chr3:162503110-162626591	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
45	nsv1008801	chr3:162503110-162628912	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
46	esv2763729	chr3:162503122-162628679	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
47	nsv1007700	chr3:162503292-162599175	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
48	esv1809546	chr3:162504152-162625640	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
49	nsv1012978	chr3:162504283-162540478	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
50	nsv1008641	chr3:162504283-162615903	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162519400-162520800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:162519800-162520800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:162520400-162520800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:162520400-162520800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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