Variant report

Variant	rs6460285
Chromosome Location	chr7:65739126-65739127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10247526	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10807701	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10807702	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950032	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12530490	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1392104	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1499613	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1499614	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1532573	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1546059	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1553174	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1873494	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1979823	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2420171	0.81[EUR][1000 genomes]
rs2420172	0.81[EUR][1000 genomes]
rs2460425	0.81[EUR][1000 genomes]
rs2460426	0.81[EUR][1000 genomes]
rs2460431	0.81[EUR][1000 genomes]
rs316304	0.81[EUR][1000 genomes]
rs4145008	0.81[EUR][1000 genomes]
rs4149468	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4236207	0.83[AMR][1000 genomes]
rs4481472	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4718309	0.81[EUR][1000 genomes]
rs4718315	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718316	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718317	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718333	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6460274	0.81[EUR][1000 genomes]
rs6958289	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6958420	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6959002	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6964245	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6964530	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6966322	0.81[EUR][1000 genomes]
rs6974723	0.81[EUR][1000 genomes]
rs7778911	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs778679	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs778683	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778687	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs778704	0.82[AMR][1000 genomes]
rs778718	0.81[AMR][1000 genomes]
rs7787230	0.81[EUR][1000 genomes]
rs778729	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs778732	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs778733	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7792391	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7804223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7808834	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs958550	0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6460285	VKORC1L1	cis	Whole Blood	GTEx
rs6460285	RP4-756H11.3	cis	lung	GTEx
rs6460285	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460285	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6460285	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs6460285	GUSB	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
2	chr7:65732000-65746800	Weak transcription	Aorta	Aorta
3	chr7:65732600-65746600	Weak transcription	Liver	Liver
4	chr7:65733000-65742000	Weak transcription	NHLF	lung
5	chr7:65733000-65744800	Weak transcription	HSMMtube	muscle
6	chr7:65733000-65745000	Weak transcription	HSMM	muscle
7	chr7:65733200-65742000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:65733200-65746800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:65733400-65745000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:65733600-65741800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:65733600-65741800	Weak transcription	NHDF-Ad	bronchial
12	chr7:65734000-65744800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:65734000-65746800	Weak transcription	Esophagus	oesophagus
14	chr7:65735200-65741800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:65735800-65740400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:65736000-65741800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:65736400-65747600	Weak transcription	Gastric	stomach
18	chr7:65736600-65741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:65736600-65741600	Weak transcription	NHEK	skin
20	chr7:65736600-65742000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:65737800-65748600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:65738000-65739600	Weak transcription	Fetal Lung	lung
23	chr7:65738000-65741400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:65738600-65740200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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