Variant report

Variant	rs9793471
Chromosome Location	chr1:47499795-47499796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:47499464-47499801	MCF10A-Er-Src	breast:	n/a	chr1:47499647-47499658
2	STAT3	chr1:47499466-47499808	MCF10A-Er-Src	breast:	n/a	chr1:47499647-47499658

Variant related genes	Relation type
CYP4X1	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1021827	0.83[MEX][hapmap]
rs10890445	0.83[MEX][hapmap]
rs10890446	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890449	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890453	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890454	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890455	0.85[AMR][1000 genomes]
rs10890457	0.87[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs10890460	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10890462	0.84[EUR][1000 genomes]
rs10890464	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10890465	0.85[EUR][1000 genomes]
rs10890466	0.84[EUR][1000 genomes]
rs10890467	0.84[EUR][1000 genomes]
rs1110425	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1117514	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211422	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11211423	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211435	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211439	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211442	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211446	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs11211450	0.85[EUR][1000 genomes]
rs11211451	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11211454	0.83[EUR][1000 genomes]
rs11211455	0.81[EUR][1000 genomes]
rs11211457	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11211459	0.82[EUR][1000 genomes]
rs12022635	0.91[CEU][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037014	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12042073	0.84[EUR][1000 genomes]
rs12046348	0.84[EUR][1000 genomes]
rs12124648	0.84[EUR][1000 genomes]
rs12404496	0.87[ASN][1000 genomes]
rs12564635	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12567857	0.82[AMR][1000 genomes]
rs12568064	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12732488	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734327	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12736235	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393659	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502908	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1553391	0.87[AMR][1000 genomes]
rs1847222	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1847223	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1847224	0.85[EUR][1000 genomes]
rs1967756	0.84[EUR][1000 genomes]
rs1967757	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2016160	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2055500	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2134471	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202219	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405580	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405588	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742079	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2798352	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs28462300	0.83[EUR][1000 genomes]
rs3117713	0.82[EUR][1000 genomes]
rs3850876	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4314923	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4375314	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4448558	1.00[JPT][hapmap]
rs4926773	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926785	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926786	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926787	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926788	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926789	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926791	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926792	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926793	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926797	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926804	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926805	0.83[EUR][1000 genomes]
rs4926806	0.80[EUR][1000 genomes]
rs4926807	0.80[EUR][1000 genomes]
rs4926809	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926826	0.85[EUR][1000 genomes]
rs4926869	0.83[EUR][1000 genomes]
rs6588388	0.81[EUR][1000 genomes]
rs6588389	0.82[EUR][1000 genomes]
rs6664392	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6664496	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6669621	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6675902	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6683137	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6690005	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6693145	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6701611	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6704068	0.81[EUR][1000 genomes]
rs7512729	0.83[EUR][1000 genomes]
rs7519903	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7522639	0.83[EUR][1000 genomes]
rs7526674	0.85[EUR][1000 genomes]
rs7540264	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7545399	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7547893	0.83[EUR][1000 genomes]
rs9326151	0.83[MEX][hapmap]
rs9326153	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9633421	0.84[EUR][1000 genomes]
rs9659815	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9699932	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701154	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701868	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701886	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701899	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728169	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729662	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs9793711	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793716	0.95[CEU][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv871080	chr1:47489786-47517123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9793471	SPATA6	cis	cerebellum	SCAN
rs9793471	AKR1A1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47490400-47500400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:47491000-47501600	Weak transcription	Gastric	stomach
3	chr1:47491600-47517200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:47496000-47501200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:47497400-47500400	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:47497400-47512400	Weak transcription	Liver	Liver
7	chr1:47497600-47503800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:47497600-47511200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:47497600-47514000	Weak transcription	Left Ventricle	heart
10	chr1:47497800-47500400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:47497800-47507200	Weak transcription	Pancreas	Pancrea
12	chr1:47497800-47516200	Weak transcription	Lung	lung
13	chr1:47497800-47516800	Weak transcription	Esophagus	oesophagus
14	chr1:47498000-47501200	Weak transcription	Fetal Brain Male	brain
15	chr1:47498600-47508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:47499000-47502000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:47499200-47500200	Weak transcription	Aorta	Aorta
18	chr1:47499600-47500600	Strong transcription	Adipose Nuclei	Adipose

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