Variant report

Variant	rs12490029
Chromosome Location	chr3:163769079-163769080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 235 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:216)

rs_ID	r²[population]
rs10446340	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513605	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10804811	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804812	0.86[ASN][1000 genomes]
rs10936395	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936396	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936397	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936399	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936400	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936401	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10936402	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10936404	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10936405	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10936406	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10936408	0.86[ASN][1000 genomes]
rs10936409	0.83[ASN][1000 genomes]
rs10936411	0.83[ASN][1000 genomes]
rs11536323	0.83[ASN][1000 genomes]
rs11543537	0.83[ASN][1000 genomes]
rs11706518	0.84[ASN][1000 genomes]
rs11706792	0.89[ASN][1000 genomes]
rs11707163	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11707867	0.84[ASN][1000 genomes]
rs11709197	0.86[ASN][1000 genomes]
rs11709561	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710319	0.86[ASN][1000 genomes]
rs11710964	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11711476	0.89[ASN][1000 genomes]
rs11711705	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11715639	0.89[ASN][1000 genomes]
rs11718123	0.86[ASN][1000 genomes]
rs11718667	0.90[ASN][1000 genomes]
rs11719283	0.85[ASN][1000 genomes]
rs11719688	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12485397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485817	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12486559	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12486777	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12486799	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487050	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487512	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12487536	0.86[ASN][1000 genomes]
rs12488755	0.84[ASN][1000 genomes]
rs12488823	0.85[ASN][1000 genomes]
rs12489284	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489384	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489447	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489450	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12489790	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12489916	0.89[ASN][1000 genomes]
rs12490006	0.86[ASN][1000 genomes]
rs12490037	0.86[ASN][1000 genomes]
rs12490057	0.86[ASN][1000 genomes]
rs12490198	0.81[ASN][1000 genomes]
rs12490826	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12490884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490894	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12492039	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492243	0.86[ASN][1000 genomes]
rs12493169	0.82[ASN][1000 genomes]
rs12493224	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12493528	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494351	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494452	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494515	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494841	0.86[ASN][1000 genomes]
rs12494921	0.83[ASN][1000 genomes]
rs12495535	0.82[ASN][1000 genomes]
rs12495977	0.86[GIH][hapmap]
rs12497290	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12497350	0.89[ASN][1000 genomes]
rs12497621	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12629383	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12631347	0.89[ASN][1000 genomes]
rs12632056	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12634584	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12636667	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12638057	0.89[ASN][1000 genomes]
rs13060391	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069803	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070113	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073107	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13078007	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13090320	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093707	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1321538	0.83[ASN][1000 genomes]
rs1321539	0.83[ASN][1000 genomes]
rs1349285	0.86[ASN][1000 genomes]
rs1349607	0.86[ASN][1000 genomes]
rs1349609	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375832	0.89[ASN][1000 genomes]
rs1375833	0.89[ASN][1000 genomes]
rs1375834	0.89[ASN][1000 genomes]
rs1375835	0.89[ASN][1000 genomes]
rs1375839	0.89[ASN][1000 genomes]
rs1375842	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1375843	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1375844	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1375845	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1375846	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1449921	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1449922	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1449932	0.89[ASN][1000 genomes]
rs1449933	0.89[ASN][1000 genomes]
rs1449934	0.89[ASN][1000 genomes]
rs1449936	0.89[ASN][1000 genomes]
rs1449937	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1449938	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1449940	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1452156	0.86[ASN][1000 genomes]
rs1452157	0.86[ASN][1000 genomes]
rs1452160	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1452161	0.86[ASN][1000 genomes]
rs1452162	0.86[ASN][1000 genomes]
rs1452165	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1452166	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1470669	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1470670	0.86[ASN][1000 genomes]
rs1470799	0.86[ASN][1000 genomes]
rs1530755	0.86[ASN][1000 genomes]
rs1551226	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551228	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551229	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551230	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551231	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580039	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1584556	0.86[ASN][1000 genomes]
rs1597402	0.86[ASN][1000 genomes]
rs1597404	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1597794	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1597795	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847620	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16847629	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16847680	0.89[ASN][1000 genomes]
rs16847692	0.89[ASN][1000 genomes]
rs16847698	0.89[ASN][1000 genomes]
rs16847734	0.82[ASN][1000 genomes]
rs1839412	0.86[ASN][1000 genomes]
rs1839413	0.89[ASN][1000 genomes]
rs1839943	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1839944	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839945	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1947343	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1992985	0.89[ASN][1000 genomes]
rs1992986	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1992987	0.89[ASN][1000 genomes]
rs2122375	0.83[ASN][1000 genomes]
rs2167122	0.83[ASN][1000 genomes]
rs2197949	0.86[ASN][1000 genomes]
rs2218768	0.86[ASN][1000 genomes]
rs2365544	0.83[ASN][1000 genomes]
rs2886468	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34346561	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34720743	0.86[ASN][1000 genomes]
rs34777371	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889124	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35297573	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35351537	0.89[ASN][1000 genomes]
rs35766450	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35883757	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35979947	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280642	0.83[ASN][1000 genomes]
rs4449321	0.83[ASN][1000 genomes]
rs4449322	0.86[ASN][1000 genomes]
rs4521233	0.85[ASN][1000 genomes]
rs4546153	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547704	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4611826	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55680832	0.84[ASN][1000 genomes]
rs55871417	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55912583	0.83[ASN][1000 genomes]
rs55922928	0.86[ASN][1000 genomes]
rs55923107	0.89[ASN][1000 genomes]
rs55943692	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56011219	0.84[ASN][1000 genomes]
rs56121628	0.86[ASN][1000 genomes]
rs56212321	0.86[ASN][1000 genomes]
rs56322923	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56408530	0.86[ASN][1000 genomes]
rs56668299	0.86[ASN][1000 genomes]
rs56739753	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56873046	0.89[ASN][1000 genomes]
rs58098647	0.89[ASN][1000 genomes]
rs59281714	0.89[ASN][1000 genomes]
rs59583312	0.83[ASN][1000 genomes]
rs59847585	0.95[ASN][1000 genomes]
rs60419632	0.86[ASN][1000 genomes]
rs66459710	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67412161	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67756427	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168268	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73168269	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73168271	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73168272	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73168273	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73170720	0.94[ASN][1000 genomes]
rs73170721	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73170722	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73170724	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73170725	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73170729	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73170739	0.89[ASN][1000 genomes]
rs73170748	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73170752	0.89[ASN][1000 genomes]
rs73170753	0.89[ASN][1000 genomes]
rs73172621	0.86[ASN][1000 genomes]
rs73172622	0.86[ASN][1000 genomes]
rs73172626	0.86[ASN][1000 genomes]
rs73172627	0.86[ASN][1000 genomes]
rs73172632	0.86[ASN][1000 genomes]
rs73172635	0.86[ASN][1000 genomes]
rs7430500	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639018	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647384	0.82[ASN][1000 genomes]
rs9647389	0.83[ASN][1000 genomes]
rs9859196	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001892	chr3:163410640-163799676	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536789	chr3:163410640-163799676	Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv877820	chr3:163557163-164167085	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv2757903	chr3:163602449-163910060	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	esv2759199	chr3:163602449-163910060	Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv428097	chr3:163602449-163910060	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv428425	chr3:163602449-163910060	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv877825	chr3:163620918-164126802	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1006270	chr3:163651905-163849686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1002992	chr3:163670436-163935375	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1012169	chr3:163673654-163911342	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv877831	chr3:163713551-163777235	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv460965	chr3:163713551-163813752	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv592434	chr3:163713551-163813752	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv997626	chr3:163747480-163883789	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv997859	chr3:163751814-163915341	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
17	nsv877833	chr3:163761825-164109377	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv428748	chr3:163767546-163809026	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1012385	chr3:163768897-163831252	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:163758400-163771800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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