Variant report

Variant	rs10447407
Chromosome Location	chr6:54151514-54151515
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	chr6:54138591..54140623-chr6:54150378..54152513,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10456680	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484644	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948805	0.88[EUR][1000 genomes]
rs10948810	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1150873	1.00[CHB][hapmap]
rs12190132	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191165	0.82[EUR][1000 genomes]
rs12193042	0.82[EUR][1000 genomes]
rs12194521	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199953	0.82[EUR][1000 genomes]
rs12201826	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206200	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12212689	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212836	0.85[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs1298143	0.84[CEU][hapmap]
rs1417390	1.00[CHB][hapmap]
rs16885122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1934790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297980	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs2754813	1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs2792644	1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs60334573	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396365	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913087	0.89[EUR][1000 genomes]
rs6913138	0.89[EUR][1000 genomes]
rs6937514	0.85[CEU][hapmap]
rs73440541	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73442548	0.81[EUR][1000 genomes]
rs7741347	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7746489	1.00[EUR][1000 genomes]
rs7755107	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765626	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7773258	0.88[EUR][1000 genomes]
rs7774316	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843827	1.00[CHB][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap]
rs9296744	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9296745	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296747	0.89[EUR][1000 genomes]
rs9349700	0.84[CEU][hapmap]
rs9357793	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9357795	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9367556	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9370276	0.85[CEU][hapmap]
rs9382311	0.85[CEU][hapmap]
rs9382318	1.00[EUR][1000 genomes]
rs9382319	1.00[EUR][1000 genomes]
rs9395920	0.85[CEU][hapmap]
rs9395924	0.87[EUR][1000 genomes]
rs9464048	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885789	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10447407	TINAG	cis	parietal	SCAN
rs10447407	GSTA3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54146000-54151600	Enhancers	NHDF-Ad	bronchial
2	chr6:54146400-54152200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:54149400-54152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:54149600-54155400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:54149800-54153600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:54150200-54151800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:54150200-54151800	Enhancers	NHEK	skin
8	chr6:54150400-54151600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:54150400-54151600	Enhancers	HMEC	breast
10	chr6:54150800-54151600	Enhancers	HSMM	muscle
11	chr6:54151200-54155400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:54151200-54155600	Weak transcription	Osteobl	bone
13	chr6:54151400-54152600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:54151400-54152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:54151400-54155400	Weak transcription	NH-A	brain
16	chr6:54151400-54155400	Weak transcription	NHLF	lung
17	chr6:54151400-54155800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:54151400-54155800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:54151400-54156000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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