Variant report

Variant	rs10253883
Chromosome Location	chr7:66061138-66061139
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	POLR2A	chr7:66059776-66062499	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66056180..66058278-chr7:66060040..66062096,2	MCF-7	breast:
2	chr7:66057440..66059000-chr7:66060580..66062147,2	K562	blood:

Variant related genes	Relation type
ENSG00000232559	TF binding region
ENSG00000232559	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10215132	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10242423	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10249404	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10255377	0.83[AMR][1000 genomes]
rs10258739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263935	0.85[AFR][1000 genomes]
rs10272357	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10272546	0.83[AFR][1000 genomes]
rs10274773	0.85[AFR][1000 genomes]
rs10278371	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10278816	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10281080	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10281646	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950044	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10950045	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11765356	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11772179	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11772264	0.83[AFR][1000 genomes]
rs11773829	0.86[AFR][1000 genomes]
rs12532355	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533585	0.81[AFR][1000 genomes]
rs12534943	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1860468	0.86[AFR][1000 genomes]
rs1860470	0.85[AFR][1000 genomes]
rs1961155	0.80[AFR][1000 genomes]
rs1968127	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2013222	0.81[EUR][1000 genomes]
rs2191268	0.86[AFR][1000 genomes]
rs2286683	0.85[AFR][1000 genomes]
rs2286684	0.85[AFR][1000 genomes]
rs2659912	0.81[AFR][1000 genomes]
rs2659916	0.81[AFR][1000 genomes]
rs2707836	0.81[AFR][1000 genomes]
rs2707849	0.81[AFR][1000 genomes]
rs28846700	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35117338	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35986979	0.84[AFR][1000 genomes]
rs3764903	0.85[AFR][1000 genomes]
rs3857686	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3857688	0.85[AFR][1000 genomes]
rs3898855	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4398788	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718378	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467809	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62467857	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6460305	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66525610	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943696	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6947808	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958520	0.80[AFR][1000 genomes]
rs6960778	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6961186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6965056	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6967809	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6968619	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977632	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71563125	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732465	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7357230	0.84[AFR][1000 genomes]
rs7782320	0.81[AFR][1000 genomes]
rs7785213	0.85[AFR][1000 genomes]
rs7788576	0.81[AFR][1000 genomes]
rs7793569	0.85[AFR][1000 genomes]
rs7807930	0.85[AFR][1000 genomes]
rs7807944	0.84[AFR][1000 genomes]
rs801190	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801191	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801193	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801196	0.82[AMR][1000 genomes]
rs801207	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10253883	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs10253883	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs10253883	RP4-756H11.3	cis	Artery Tibial	GTEx
rs10253883	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs10253883	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs10253883	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs10253883	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs10253883	RP4-756H11.3	cis	lung	GTEx
rs10253883	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs10253883	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10253883	RP4-756H11.3	cis	Artery Aorta	GTEx
rs10253883	GTF2IRD1P1	cis	Thyroid	GTEx
rs10253883	RP4-756H11.3	cis	Thyroid	GTEx
rs10253883	RP4-756H11.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66057600-66067600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66058000-66062000	Weak transcription	Colonic Mucosa	Colon
3	chr7:66058000-66067600	Weak transcription	Lung	lung
4	chr7:66058200-66061600	Weak transcription	Fetal Intestine Large	intestine
5	chr7:66058200-66061600	Weak transcription	HepG2	liver
6	chr7:66058200-66062200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:66058200-66067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:66058200-66068800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:66058600-66062800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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