Variant report

Variant	rs3764904
Chromosome Location	chr7:66098384-66098385
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	chr7:66091920..66094757-chr7:66096200..66098462,2	K562	blood:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10081172	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10224189	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10224536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10225392	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10226294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10228381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229580	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10231860	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10235037	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10236665	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10237244	1.00[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs10239200	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10240153	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10240582	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10241395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10243608	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10244459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10244602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10247324	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10247852	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10252133	0.84[EUR][1000 genomes]
rs10255813	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256117	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10257393	0.84[EUR][1000 genomes]
rs10264619	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10265154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10266041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267834	0.87[EUR][1000 genomes]
rs10270326	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271177	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10273320	0.88[EUR][1000 genomes]
rs10273402	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10275413	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10277231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278343	0.88[EUR][1000 genomes]
rs10278763	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10280431	0.83[EUR][1000 genomes]
rs10280717	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10281734	0.84[EUR][1000 genomes]
rs10282522	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10479728	0.88[EUR][1000 genomes]
rs1060527	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1064795	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap]
rs12234826	0.88[EUR][1000 genomes]
rs12333749	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12334214	0.84[EUR][1000 genomes]
rs13437901	0.84[EUR][1000 genomes]
rs16868546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17138208	0.84[EUR][1000 genomes]
rs17138274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1882656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1882657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1895134	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2013707	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2420598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs28368585	0.88[EUR][1000 genomes]
rs28375318	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28379824	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28455065	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28474923	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28526115	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28533332	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28547918	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28606020	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28607736	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28615327	0.81[EUR][1000 genomes]
rs28634091	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28657758	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28663128	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3757419	0.81[EUR][1000 genomes]
rs3778908	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3800814	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814464	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823607	0.84[EUR][1000 genomes]
rs3962133	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4587218	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57774708	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57902746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58123804	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58973756	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59079543	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60026498	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60344524	0.85[ASN][1000 genomes]
rs61093354	0.80[EUR][1000 genomes]
rs61700307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6949083	0.84[EUR][1000 genomes]
rs6964080	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6973897	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6974601	0.88[EUR][1000 genomes]
rs73133809	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73133816	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133851	0.89[EUR][1000 genomes]
rs73133859	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73133865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135909	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135960	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135973	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137960	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137963	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137978	0.88[ASN][1000 genomes]
rs73139941	0.84[EUR][1000 genomes]
rs73139976	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73148698	0.80[EUR][1000 genomes]
rs73152719	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9654843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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	esv2761151	chr7:66095738-66138285	Flanking Active TSS Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3764904	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs3764904	VKORC1L1	cis	lymphoblastoid	seeQTL
rs3764904	GS1-124K5.12	cis	Artery Tibial	GTEx
rs3764904	CRCP	cis	parietal	SCAN
rs3764904	GS1-124K5.12	cis	lung	GTEx
rs3764904	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs3764904	ZNF273	cis	parietal	SCAN
rs3764904	GUSB	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66094400-66103200	Weak transcription	Small Intestine	intestine
2	chr7:66094800-66098400	Enhancers	Primary B cells from peripheral blood	blood
3	chr7:66094800-66103400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:66095000-66098400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:66095000-66099200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:66095000-66099400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:66095000-66099400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:66095000-66099400	Weak transcription	Aorta	Aorta
9	chr7:66095000-66099600	Weak transcription	A549	lung
10	chr7:66095000-66101000	Weak transcription	NHEK	skin
11	chr7:66095000-66102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:66095000-66103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:66095000-66103000	Weak transcription	Fetal Kidney	kidney
14	chr7:66095000-66103000	Weak transcription	Fetal Lung	lung
15	chr7:66095000-66103200	Weak transcription	Psoas Muscle	Psoas
16	chr7:66095000-66103400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:66095000-66103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:66095000-66103400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:66095000-66104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:66095000-66108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:66095000-66109000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr7:66095000-66115200	Weak transcription	HMEC	breast
23	chr7:66095200-66098400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr7:66095200-66098600	Weak transcription	Liver	Liver
25	chr7:66095200-66099000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:66095200-66099400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:66095200-66099400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:66095200-66099800	Weak transcription	Colonic Mucosa	Colon
29	chr7:66095200-66101000	Weak transcription	NHDF-Ad	bronchial
30	chr7:66095200-66103000	Weak transcription	Stomach Mucosa	stomach
31	chr7:66095200-66103200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:66095200-66118400	Weak transcription	Fetal Heart	heart
33	chr7:66095200-66118400	Weak transcription	HUVEC	blood vessel
34	chr7:66095400-66098400	Weak transcription	Placenta	Placenta
35	chr7:66095400-66099400	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:66095400-66101000	Weak transcription	NH-A	brain
37	chr7:66095400-66103200	Weak transcription	Pancreas	Pancrea
38	chr7:66095800-66099200	Weak transcription	Brain Substantia Nigra	brain
39	chr7:66095800-66100800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:66095800-66101000	Weak transcription	HSMM	muscle
41	chr7:66095800-66101000	Weak transcription	K562	blood
42	chr7:66095800-66102800	Weak transcription	Fetal Brain Male	brain
43	chr7:66095800-66103200	Weak transcription	Esophagus	oesophagus
44	chr7:66096000-66099400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr7:66096000-66113800	Strong transcription	Fetal Stomach	stomach
46	chr7:66096200-66099200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:66096200-66101000	Weak transcription	NHLF	lung
48	chr7:66097000-66098800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr7:66097000-66099000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:66097000-66099400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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