Variant report

Variant	rs6490281
Chromosome Location	chr12:120452826-120452827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120426318..120428272-chr12:120451574..120453127,2	MCF-7	breast:
2	chr12:120447212..120449206-chr12:120452200..120454968,2	MCF-7	breast:
3	chr12:120451212..120453577-chr12:120455749..120457974,2	MCF-7	breast:
4	chr12:120451912..120458058-chr12:120461710..120466479,5	K562	blood:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10128766	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10400498	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs10400560	0.85[ASN][1000 genomes]
rs10744747	0.83[ASN][1000 genomes]
rs10849731	0.89[ASN][1000 genomes]
rs10849732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849735	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849736	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs11064986	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11064987	0.88[ASN][1000 genomes]
rs11064988	0.89[ASN][1000 genomes]
rs11064996	0.89[ASN][1000 genomes]
rs11064998	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065003	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs11065004	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11065014	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065017	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11065018	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12310269	0.89[ASN][1000 genomes]
rs12310591	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12311327	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12318774	0.89[ASN][1000 genomes]
rs12320072	0.84[EUR][1000 genomes]
rs12320793	0.87[ASN][1000 genomes]
rs12322236	0.89[ASN][1000 genomes]
rs12422923	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16949901	0.85[ASN][1000 genomes]
rs16949946	0.82[CHB][hapmap]
rs2239200	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs2239201	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2239202	0.81[CHB][hapmap]
rs2240311	0.84[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2283361	0.81[ASN][1000 genomes]
rs2286040	0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2393570	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2893812	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs3742044	0.87[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3852586	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3852588	0.81[AMR][1000 genomes]
rs3886910	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4105713	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351876	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767869	0.89[ASN][1000 genomes]
rs4767870	0.84[ASN][1000 genomes]
rs4767871	0.85[ASN][1000 genomes]
rs4767872	0.85[ASN][1000 genomes]
rs4767873	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4767875	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767876	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs58272825	0.85[ASN][1000 genomes]
rs60466490	0.85[ASN][1000 genomes]
rs6490278	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6490280	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6490283	0.81[AMR][1000 genomes]
rs6490284	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs7295717	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7298183	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7298727	0.89[ASN][1000 genomes]
rs7300023	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7302874	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7304325	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs7305625	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7306739	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7312811	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312971	0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7314959	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7397339	0.85[ASN][1000 genomes]
rs7956436	0.86[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7958402	0.89[ASN][1000 genomes]
rs7958497	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.92[ASN][1000 genomes]
rs7960725	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7961738	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7962812	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7965829	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs7968557	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7971249	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7977281	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7978927	0.85[EUR][1000 genomes];0.84[ASN][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120428600-120453200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:120437800-120462400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:120445600-120453200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:120447400-120454600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:120447600-120454200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:120447600-120454200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr12:120447800-120454200	Enhancers	Primary T cells from cord blood	blood
8	chr12:120448400-120454200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:120448400-120454200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:120448600-120454000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:120449200-120453000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:120450000-120454400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:120450000-120454600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:120450200-120453000	Enhancers	Fetal Thymus	thymus
15	chr12:120450400-120456000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:120451200-120453000	Enhancers	Hela-S3	cervix
17	chr12:120451200-120453600	Enhancers	HepG2	liver
18	chr12:120451800-120453000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:120451800-120454000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:120452000-120453400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:120452000-120465000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:120452200-120454200	Enhancers	GM12878-XiMat	blood
23	chr12:120452200-120475200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:120452400-120454400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr12:120452800-120453200	Enhancers	Thymus	Thymus

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