Variant report

Variant	rs2193662
Chromosome Location	chr12:46984370-46984371
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs10880975	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10880976	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs10880977	1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10880980	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11183464	1.00[CEU][hapmap]
rs11183497	1.00[CEU][hapmap]
rs11183507	0.83[AMR][1000 genomes]
rs11183524	0.91[EUR][1000 genomes]
rs11183527	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11183536	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11183539	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183547	0.84[EUR][1000 genomes]
rs11183550	0.84[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap]
rs11830099	0.86[EUR][1000 genomes]
rs11830501	0.86[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11831920	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11832316	0.86[EUR][1000 genomes]
rs11833393	0.91[EUR][1000 genomes]
rs11834607	0.91[EUR][1000 genomes]
rs11835517	0.86[EUR][1000 genomes]
rs11835974	0.86[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11836940	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11837104	0.86[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12301825	0.87[MEX][hapmap]
rs12305921	1.00[CEU][hapmap]
rs12310635	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12579348	0.86[EUR][1000 genomes]
rs12579976	0.86[EUR][1000 genomes]
rs12580092	0.86[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12582056	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12582305	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17096991	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17096995	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17097009	0.86[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[EUR][1000 genomes]
rs17121410	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17121412	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1946175	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2042058	1.00[CEU][hapmap]
rs2193663	0.86[EUR][1000 genomes]
rs2216439	0.83[EUR][1000 genomes]
rs235601	0.84[EUR][1000 genomes]
rs235602	0.84[EUR][1000 genomes]
rs235607	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs235610	0.84[EUR][1000 genomes]
rs235617	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs235621	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs235622	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs235625	0.81[EUR][1000 genomes]
rs235626	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs235627	0.81[EUR][1000 genomes]
rs2408576	0.86[EUR][1000 genomes]
rs2408577	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2430937	0.91[EUR][1000 genomes]
rs2430939	0.91[EUR][1000 genomes]
rs2430940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2430941	0.91[EUR][1000 genomes]
rs2430942	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2430943	0.91[EUR][1000 genomes]
rs2430946	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2471583	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2471588	0.91[EUR][1000 genomes]
rs2471594	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2471601	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2471602	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2471605	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2471608	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2471617	0.91[EUR][1000 genomes]
rs2471618	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs28768973	0.91[EUR][1000 genomes]
rs2897969	0.83[EUR][1000 genomes]
rs2909411	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2960450	0.91[EUR][1000 genomes]
rs34008890	0.81[EUR][1000 genomes]
rs35096979	0.81[EUR][1000 genomes]
rs4604970	0.86[EUR][1000 genomes]
rs4768124	0.82[MEX][hapmap]
rs4768125	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768731	0.86[AMR][1000 genomes]
rs4768735	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs4768741	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768744	1.00[CEU][hapmap]
rs56152575	0.86[EUR][1000 genomes]
rs56181923	0.86[EUR][1000 genomes]
rs56271434	0.86[EUR][1000 genomes]
rs57370043	0.81[EUR][1000 genomes]
rs57439008	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57658610	0.91[EUR][1000 genomes]
rs58449317	0.86[EUR][1000 genomes]
rs58503088	0.86[EUR][1000 genomes]
rs58561072	0.81[EUR][1000 genomes]
rs58813899	0.86[EUR][1000 genomes]
rs59521025	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59903937	0.86[EUR][1000 genomes]
rs60191997	0.91[EUR][1000 genomes]
rs60669661	0.86[EUR][1000 genomes]
rs60681792	0.86[EUR][1000 genomes]
rs61072098	0.87[EUR][1000 genomes]
rs61355826	0.91[EUR][1000 genomes]
rs61641663	0.81[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7138914	0.86[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7308386	0.86[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs73282109	0.81[EUR][1000 genomes]
rs73290402	0.86[EUR][1000 genomes]
rs73291964	0.86[EUR][1000 genomes]
rs73291976	0.86[EUR][1000 genomes]
rs73291980	0.86[EUR][1000 genomes]
rs73292000	0.86[EUR][1000 genomes]
rs73292001	0.91[EUR][1000 genomes]
rs73293911	0.86[EUR][1000 genomes]
rs73293919	0.86[EUR][1000 genomes]
rs7488464	0.91[EUR][1000 genomes]
rs765707	0.86[EUR][1000 genomes]
rs7976710	0.86[EUR][1000 genomes]
rs9669050	0.91[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs9783500	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9971651	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases
5	esv1811918	chr12:46965257-47033254	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46972400-46984400	Weak transcription	NHEK	skin
2	chr12:46973600-46985200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:46980000-46984600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:46980000-46984800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:46980000-46989000	Weak transcription	Primary B cells from cord blood	blood
6	chr12:46980200-46984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:46980200-46984600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:46980200-46984800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:46980200-46984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:46980200-46984800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:46980200-46984800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:46980200-46984800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:46980200-46984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:46980200-46984800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:46980200-46984800	Weak transcription	Esophagus	oesophagus
16	chr12:46980200-46985000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:46980200-46985000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:46980200-46986800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:46980200-46995600	Weak transcription	Gastric	stomach
20	chr12:46980200-47002000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:46980200-47002200	Weak transcription	Thymus	Thymus
22	chr12:46980200-47002800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:46980400-46984400	Weak transcription	HepG2	liver
24	chr12:46980400-46995000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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