Variant report

Variant	rs6460307
Chromosome Location	chr7:66060871-66060872
allele	A/G
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: 54 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10107	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10233806	0.89[CEU][hapmap];0.94[YRI][hapmap]
rs10244498	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs10278014	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10281499	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11761542	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11772819	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs12532998	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs12673450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12698520	0.88[CEU][hapmap]
rs13308803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13536	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1638735	0.81[YRI][hapmap]
rs1860469	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1962050	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap]
rs1968225	0.89[CEU][hapmap]
rs2003300	0.94[YRI][hapmap]
rs2013908	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2077593	0.89[CEU][hapmap]
rs2109297	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2659892	0.95[CEU][hapmap]
rs2659893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2707824	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2707851	0.81[YRI][hapmap]
rs3735148	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs3778909	0.83[YRI][hapmap]
rs3846973	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4718383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6460296	0.89[CEU][hapmap]
rs6460302	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6460304	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6945019	0.89[CEU][hapmap]
rs6945032	0.89[CEU][hapmap]
rs6947339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs6950137	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6951302	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6955837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6962717	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6976714	0.96[LWK][hapmap];0.88[YRI][hapmap]
rs778697	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs778702	1.00[CEU][hapmap]
rs7789768	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs7800620	1.00[ASW][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs801195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs801204	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs964971	0.81[YRI][hapmap]
rs974239	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs9791713	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]

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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs6460307	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460307	ASL	cis	cerebellum	SCAN
rs6460307	GS1-124K5.4	cis	Esophagus Muscularis	GTEx
rs6460307	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460307	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6460307	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460307	LINC00174	cis	Thyroid	GTEx
rs6460307	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6460307	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6460307	RABGEF1	cis	parietal	SCAN
rs6460307	GTF2IRD1P1	cis	Thyroid	GTEx
rs6460307	VKORC1L1	cis	multi-tissue	Pritchard
rs6460307	RP4-756H11.3	cis	Thyroid	GTEx
rs6460307	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460307	TPST1	cis	multi-tissue	Pritchard
rs6460307	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6460307	GS1-124K5.4	cis	Stomach	GTEx
rs6460307	RP4-756H11.3	cis	lung	GTEx
rs6460307	TPST1	cis	lymphoblastoid	seeQTL
rs6460307	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6460307	RNU6-96P	cis	Thyroid	GTEx
rs6460307	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460307	LOC493754	cis	normal skin	skin_eQTL
rs6460307	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6460307	CRCP	cis	parietal	SCAN
rs6460307	GS1-124K5.11	cis	Thyroid	GTEx
rs6460307	ZNF117	cis	parietal	SCAN
rs6460307	GS1-124K5.2	cis	Whole Blood	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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