Variant report

Variant	rs1404820
Chromosome Location	chr12:47538131-47538132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10785659	0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs10881049	0.89[EUR][1000 genomes]
rs10881050	0.87[EUR][1000 genomes]
rs10881051	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10881053	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612285	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371765	0.82[CEU][hapmap]
rs12578367	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579796	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12810420	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404812	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404813	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404814	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404821	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525452	0.83[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1581560	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917662	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917663	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091295	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222609	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408714	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408715	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529959	0.83[EUR][1000 genomes]
rs4533118	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4544084	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598738	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768775	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55651541	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7484989	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958186	0.81[TSI][hapmap]
rs9634260	0.86[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47505800-47538600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:47506200-47538400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:47508400-47545200	Weak transcription	HSMMtube	muscle
4	chr12:47517400-47538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:47527000-47547800	Weak transcription	Ovary	ovary
6	chr12:47529600-47542600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:47533400-47541800	Weak transcription	Osteobl	bone
8	chr12:47533600-47538600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:47533600-47538600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:47533600-47542200	Weak transcription	Spleen	Spleen
11	chr12:47533800-47542200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:47535800-47538200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:47535800-47549600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:47535800-47554600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:47536000-47540400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:47536000-47549600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:47536000-47550000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:47536000-47550200	Weak transcription	Adipose Nuclei	Adipose
19	chr12:47536000-47550200	Weak transcription	Aorta	Aorta
20	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:47536200-47538200	Weak transcription	Primary T cells from cord blood	blood
22	chr12:47536200-47538400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:47536200-47538800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:47536200-47564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:47536400-47549400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:47537400-47538800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:47537600-47540000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:47538000-47539800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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