Variant report

Variant	rs988913
Chromosome Location	chr6:54756308-54756309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54742187..54744014-chr6:54753985..54756805,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10456176	0.81[CHB][hapmap]
rs10485136	0.95[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10948866	0.88[CHB][hapmap]
rs1108887	0.84[ASN][1000 genomes]
rs1108888	0.84[ASN][1000 genomes]
rs1115159	0.82[CHB][hapmap]
rs1155749	0.82[CHB][hapmap]
rs12192659	0.81[CHB][hapmap]
rs12525787	0.84[EUR][1000 genomes]
rs12662124	0.85[EUR][1000 genomes]
rs1354288	0.84[ASN][1000 genomes]
rs1393775	0.84[ASN][1000 genomes]
rs1393776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1472679	0.88[CHB][hapmap]
rs148109	0.82[CHD][hapmap]
rs1503134	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1503136	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1503140	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1503146	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1503147	0.95[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566723	0.83[EUR][1000 genomes]
rs1580891	0.84[ASN][1000 genomes]
rs1580892	0.84[ASN][1000 genomes]
rs171224	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs181155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1910350	0.84[ASN][1000 genomes]
rs1963697	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064432	0.85[EUR][1000 genomes]
rs2134537	0.84[ASN][1000 genomes]
rs2134538	0.84[ASN][1000 genomes]
rs2174115	0.84[ASN][1000 genomes]
rs2179786	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2207025	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2207026	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs239781	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs239783	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs239790	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs239794	0.83[CHD][hapmap]
rs239796	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs239801	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239837	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816810	0.82[JPT][hapmap]
rs2816811	0.83[CHD][hapmap]
rs2816812	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3125261	0.83[ASN][1000 genomes]
rs3125263	0.84[ASN][1000 genomes]
rs3125267	0.84[ASN][1000 genomes]
rs3125269	0.84[ASN][1000 genomes]
rs4141552	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4712081	0.90[CEU][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4712082	0.83[EUR][1000 genomes]
rs4712083	0.84[ASN][1000 genomes]
rs4715492	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6459034	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6459035	0.90[EUR][1000 genomes]
rs6902245	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6902422	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6908170	0.83[EUR][1000 genomes]
rs6918402	0.81[CHB][hapmap]
rs6922186	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6929930	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6937970	0.81[CHB][hapmap]
rs6939778	0.85[EUR][1000 genomes]
rs72645372	0.84[EUR][1000 genomes]
rs7453866	0.82[CHB][hapmap]
rs7741915	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7744592	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7761336	0.82[CHB][hapmap]
rs7764641	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7765236	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7765721	0.87[CHB][hapmap]
rs924712	0.82[CHB][hapmap]
rs9296771	0.85[EUR][1000 genomes]
rs931766	0.88[CHB][hapmap]
rs932452	0.90[CEU][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes]
rs9349740	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357822	0.90[EUR][1000 genomes]
rs9367597	0.90[CEU][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs9370344	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9370345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382396	0.88[EUR][1000 genomes]
rs9382397	0.85[EUR][1000 genomes]
rs9382398	0.84[EUR][1000 genomes]
rs9382402	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382404	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382407	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382408	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9396006	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9396007	0.84[EUR][1000 genomes]
rs9396011	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9475068	0.84[EUR][1000 genomes]
rs9475069	0.81[EUR][1000 genomes]
rs9475078	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9475081	0.82[EUR][1000 genomes]
rs960834	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs960835	0.83[EUR][1000 genomes]
rs971526	0.88[CHB][hapmap]
rs973205	0.88[CHB][hapmap]
rs980821	0.84[ASN][1000 genomes]
rs980822	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:54746400-54757800	Weak transcription	Hela-S3	cervix
5	chr6:54752200-54759000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:54752400-54758600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:54755200-54756600	Enhancers	NHEK	skin
8	chr6:54755800-54757200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:54755800-54758000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:54755800-54758000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:54756000-54757200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:54756200-54757000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:54756200-54758400	Enhancers	HMEC	breast

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