Variant report

Variant	rs12490728
Chromosome Location	chr3:162331961-162331962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1031836	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804798	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12487308	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489510	0.88[ASN][1000 genomes]
rs1390791	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564173	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17706800	0.88[ASN][1000 genomes]
rs17707047	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17757752	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845914	0.81[ASN][1000 genomes]
rs1871112	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1871113	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1908781	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088316	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088317	0.85[ASN][1000 genomes]
rs2101909	0.89[ASN][1000 genomes]
rs2126850	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2132623	0.83[ASN][1000 genomes]
rs2132624	0.85[ASN][1000 genomes]
rs2132625	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132626	0.87[ASN][1000 genomes]
rs2169727	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2173069	0.85[ASN][1000 genomes]
rs2173070	0.87[ASN][1000 genomes]
rs2173071	0.87[ASN][1000 genomes]
rs2201661	0.85[ASN][1000 genomes]
rs2361602	0.85[ASN][1000 genomes]
rs28754663	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28795418	0.88[ASN][1000 genomes]
rs28846818	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3898995	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943312	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4059921	0.88[ASN][1000 genomes]
rs55982102	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58201033	0.85[ASN][1000 genomes]
rs58711228	0.85[ASN][1000 genomes]
rs59675759	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441519	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6441525	0.88[ASN][1000 genomes]
rs6441526	0.88[ASN][1000 genomes]
rs6441527	0.88[ASN][1000 genomes]
rs6441528	0.87[ASN][1000 genomes]
rs6441529	0.87[ASN][1000 genomes]
rs6765585	0.87[ASN][1000 genomes]
rs6766662	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs67928366	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804879	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs721810	0.85[ASN][1000 genomes]
rs73029660	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73163573	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73163590	0.88[ASN][1000 genomes]
rs73163599	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73163601	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7430269	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7610021	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611213	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7623893	0.87[ASN][1000 genomes]
rs7634164	0.87[ASN][1000 genomes]
rs7639764	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641871	0.85[ASN][1000 genomes]
rs7642075	0.85[ASN][1000 genomes]
rs7642378	0.85[ASN][1000 genomes]
rs7642986	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7643080	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7652013	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs766807	0.85[ASN][1000 genomes]
rs766809	0.85[ASN][1000 genomes]
rs766810	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924153	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924154	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814657	0.85[ASN][1000 genomes]
rs9825364	0.85[ASN][1000 genomes]
rs9829208	0.80[ASN][1000 genomes]
rs9830708	0.85[ASN][1000 genomes]
rs9830875	0.85[ASN][1000 genomes]
rs9832115	0.87[ASN][1000 genomes]
rs9850449	0.85[ASN][1000 genomes]
rs9859466	0.88[ASN][1000 genomes]
rs9865002	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

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	nsv877735	chr3:162123179-162380954	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv829775	chr3:162211618-162406402	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	nsv877755	chr3:162218849-162386891	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS 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
9	nsv877756	chr3:162218849-162391801	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv877757	chr3:162226534-162391801	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1005142	chr3:162284967-162447818	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	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
14	nsv592206	chr3:162305516-162380954	Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv592207	chr3:162310379-162391801	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv877760	chr3:162314038-162391801	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv980026	chr3:162328570-162359238	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162317800-162332400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:162328400-162332200	Weak transcription	Dnd41	blood

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