Variant report

Variant	rs6960476
Chromosome Location	chr7:65733113-65733114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65728235..65729776-chr7:65732042..65733937,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1002053	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10215948	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10257427	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10267430	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10755833	0.82[EUR][1000 genomes]
rs11765965	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11974219	0.83[EUR][1000 genomes]
rs11974264	0.82[EUR][1000 genomes]
rs12668936	0.82[EUR][1000 genomes]
rs12673810	0.81[EUR][1000 genomes]
rs12698520	0.81[EUR][1000 genomes]
rs13225383	0.82[EUR][1000 genomes]
rs13227219	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1363055	0.81[EUR][1000 genomes]
rs1540651	0.81[EUR][1000 genomes]
rs1565531	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1643395	0.86[EUR][1000 genomes]
rs1695815	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1807064	0.81[AMR][1000 genomes]
rs1833495	0.81[EUR][1000 genomes]
rs1968225	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036264	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2077593	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2173570	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2420591	0.82[EUR][1000 genomes]
rs2420599	0.80[EUR][1000 genomes]
rs28682868	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35028832	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3935391	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4717292	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4717299	0.81[EUR][1000 genomes]
rs4718343	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718344	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718349	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55748098	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460291	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6460292	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460295	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460296	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460300	0.81[EUR][1000 genomes]
rs6945019	0.81[EUR][1000 genomes]
rs6945032	0.81[EUR][1000 genomes]
rs6945843	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949920	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6956179	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6961155	0.81[EUR][1000 genomes]
rs6961990	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6963646	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6971509	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6977501	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6979382	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs709595	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709597	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7781061	0.81[EUR][1000 genomes]
rs7783613	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778682	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs778685	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778689	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778692	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778694	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778695	0.84[AMR][1000 genomes]
rs778699	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778700	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778706	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778708	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778709	0.83[EUR][1000 genomes]
rs778710	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778712	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778721	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778723	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778726	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778727	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778731	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778735	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7788984	0.81[EUR][1000 genomes]
rs7789768	0.81[EUR][1000 genomes]
rs7791891	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7794930	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7799834	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7803424	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937495	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9691480	0.81[EUR][1000 genomes]
rs9969301	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9986696	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6960476	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6960476	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6960476	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6960476	GS1-124K5.4	cis	Whole Blood	GTEx
rs6960476	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6960476	GS1-124K5.4	cis	Stomach	GTEx
rs6960476	RNU6-96P	cis	Thyroid	GTEx
rs6960476	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6960476	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6960476	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6960476	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6960476	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6960476	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6960476	GS1-124K5.11	cis	Thyroid	GTEx
rs6960476	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6960476	RP4-756H11.3	cis	Thyroid	GTEx
rs6960476	RP4-756H11.3	cis	lung	GTEx
rs6960476	GTF2IRD1P1	cis	Thyroid	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
2	chr7:65731800-65733200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:65731800-65733400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:65731800-65733400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:65731800-65735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:65732000-65734400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:65732000-65746800	Weak transcription	Aorta	Aorta
8	chr7:65732600-65733400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:65732600-65733600	Enhancers	NHDF-Ad	bronchial
10	chr7:65732600-65746600	Weak transcription	Liver	Liver
11	chr7:65732800-65733200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr7:65732800-65733400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:65732800-65733600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:65732800-65733600	Enhancers	Osteobl	bone
15	chr7:65733000-65733200	Enhancers	Ovary	ovary
16	chr7:65733000-65733400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:65733000-65733600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:65733000-65734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:65733000-65735200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:65733000-65736600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:65733000-65736600	Weak transcription	Fetal Lung	lung
22	chr7:65733000-65737400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:65733000-65742000	Weak transcription	NHLF	lung
24	chr7:65733000-65744800	Weak transcription	HSMMtube	muscle
25	chr7:65733000-65745000	Weak transcription	HSMM	muscle

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