Variant report

Variant	rs6964530
Chromosome Location	chr7:65718851-65718852
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65715302..65717280-chr7:65718267..65720780,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10247526	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807701	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807702	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10950032	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12530490	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13235972	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13308751	0.81[AFR][1000 genomes]
rs1392104	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1499613	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1499614	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1532573	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1546059	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553174	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs186378	0.81[AFR][1000 genomes]
rs1873494	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979823	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420170	0.82[AMR][1000 genomes]
rs2420171	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420172	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2460422	0.81[AFR][1000 genomes]
rs2460425	0.84[EUR][1000 genomes]
rs2460426	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2460431	0.84[EUR][1000 genomes]
rs2465120	0.82[EUR][1000 genomes]
rs313819	0.81[AFR][1000 genomes]
rs313822	0.81[AFR][1000 genomes]
rs316304	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs316318	0.81[AFR][1000 genomes]
rs316326	0.81[AFR][1000 genomes]
rs316334	0.81[AFR][1000 genomes]
rs34192067	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34700450	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs36104268	1.00[AFR][1000 genomes]
rs4145008	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4149468	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs422164	0.81[AFR][1000 genomes]
rs4236207	0.86[AMR][1000 genomes]
rs4481472	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4718309	0.84[EUR][1000 genomes]
rs4718315	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718316	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718317	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718333	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58669269	0.91[AFR][1000 genomes]
rs6460274	0.84[EUR][1000 genomes]
rs6460277	0.81[EUR][1000 genomes]
rs6460285	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6958289	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6958420	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6959002	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6964245	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966322	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6974723	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7778911	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778679	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778683	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778687	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778691	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778693	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778701	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778704	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778717	0.82[ASN][1000 genomes]
rs778718	0.84[AMR][1000 genomes]
rs7787230	0.84[EUR][1000 genomes]
rs778729	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778732	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778733	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7792391	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7804223	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7808834	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958550	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9769882	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6964530	RP4-756H11.3	cis	lung	GTEx
rs6964530	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6964530	ASL	cis	multi-tissue	Pritchard
rs6964530	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs6964530	VKORC1L1	cis	Whole Blood	GTEx
rs6964530	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6964530	GUSB	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65701600-65729200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr7:65702400-65723600	Weak transcription	Gastric	stomach
4	chr7:65704000-65726800	Weak transcription	HSMM	muscle
5	chr7:65704200-65729200	Weak transcription	Aorta	Aorta
6	chr7:65704200-65731200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:65704400-65720200	Weak transcription	HSMMtube	muscle
8	chr7:65704400-65721800	Weak transcription	Fetal Intestine Small	intestine
9	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
10	chr7:65704800-65720200	Weak transcription	NHLF	lung
11	chr7:65705800-65729200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:65706000-65720200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:65706200-65720200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:65706400-65720200	Weak transcription	NHDF-Ad	bronchial
15	chr7:65707000-65721200	Weak transcription	Fetal Kidney	kidney
16	chr7:65709800-65723400	Weak transcription	Ovary	ovary
17	chr7:65710600-65720200	Weak transcription	Brain Angular Gyrus	brain
18	chr7:65711800-65720400	Weak transcription	Fetal Lung	lung
19	chr7:65711800-65723200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:65711800-65723200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:65712800-65721800	Weak transcription	Left Ventricle	heart
22	chr7:65712800-65729200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:65714600-65720600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:65715200-65721200	Weak transcription	Liver	Liver
25	chr7:65715200-65723200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:65715600-65722400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:65716000-65720200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:65716000-65720400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:65716000-65721400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:65716200-65720200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:65716200-65723600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:65716400-65720200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:65716600-65720000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:65716600-65720000	Weak transcription	Osteobl	bone
35	chr7:65716600-65720200	Weak transcription	NH-A	brain
36	chr7:65716600-65721400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:65716800-65719600	Weak transcription	HepG2	liver
38	chr7:65716800-65719800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:65716800-65719800	Weak transcription	HMEC	breast
40	chr7:65716800-65720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:65716800-65720200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:65716800-65720200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:65716800-65720200	Weak transcription	NHEK	skin
44	chr7:65718000-65723200	Weak transcription	Brain Anterior Caudate	brain
45	chr7:65718400-65719200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:65718400-65719400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:65718600-65723200	Enhancers	Primary neutrophils fromperipheralblood	blood

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