Variant report

Variant	rs6958484
Chromosome Location	chr7:65599446-65599447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65549975..65551527-chr7:65598587..65601084,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1000464	0.88[CEU][hapmap]
rs1002053	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs10215948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs10224872	0.88[CEU][hapmap]
rs10228885	0.88[CEU][hapmap]
rs10240249	0.81[AMR][1000 genomes]
rs10247043	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10250544	0.80[GIH][hapmap]
rs10256544	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs10257427	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10260426	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs10261398	0.88[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs10267430	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10268656	0.81[AMR][1000 genomes]
rs10271553	0.84[AMR][1000 genomes]
rs10272021	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10282433	0.88[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs10447522	0.88[CEU][hapmap]
rs1129531	0.82[CHB][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes]
rs1144894	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1144895	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1167390	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes]
rs1167395	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1167406	0.88[CEU][hapmap]
rs1167411	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1167612	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11760844	0.88[CEU][hapmap]
rs1182882	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1183245	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11971949	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11974219	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11974264	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11984115	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs12537823	0.88[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs13225383	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13229046	0.80[ASN][1000 genomes]
rs13240492	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13245728	0.80[YRI][hapmap]
rs13247295	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1540651	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565531	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs160635	0.82[AMR][1000 genomes]
rs1612452	0.83[AMR][1000 genomes]
rs1616988	0.81[AMR][1000 genomes]
rs1875057	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs1976200	0.80[YRI][hapmap]
rs1983372	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2087647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088655	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs2173570	1.00[CEU][hapmap]
rs2220626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2249458	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs2420168	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28470208	0.85[AMR][1000 genomes]
rs28682868	0.81[AMR][1000 genomes]
rs2901152	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs2949696	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35028832	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35034167	0.85[AMR][1000 genomes]
rs4149461	0.88[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs4236208	0.88[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs4368860	0.85[AMR][1000 genomes]
rs4612218	0.82[AMR][1000 genomes]
rs4718330	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs55962648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57866200	0.84[AMR][1000 genomes]
rs587360	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs59466412	0.84[AMR][1000 genomes]
rs6460269	0.81[YRI][hapmap]
rs6460282	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs6944374	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs6945843	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6946143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6951503	0.84[CEU][hapmap]
rs6952182	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs6957690	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960446	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs6961717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6963646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6964437	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs6971509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap]
rs6974614	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs697968	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs697969	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs697970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs709608	0.81[AMR][1000 genomes]
rs709609	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs736270	0.87[ASW][hapmap]
rs7783779	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs7786892	0.85[AMR][1000 genomes]
rs7794930	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap]
rs7798630	0.88[CEU][hapmap]
rs7801282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs780742	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs780743	0.89[AMR][1000 genomes]
rs780744	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7809814	0.86[AMR][1000 genomes]
rs780998	0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809080	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs875971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880166	0.88[CEU][hapmap]
rs908915	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes]
rs937495	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap]
rs949930	0.88[CEU][hapmap]
rs9986696	0.81[AMR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv971489	chr7:65590579-65614004	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6958484	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6958484	GS1-124K5.4	cis	Whole Blood	GTEx
rs6958484	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6958484	GTF2IRD1P1	cis	Thyroid	GTEx
rs6958484	RNU6-96P	cis	Thyroid	GTEx
rs6958484	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6958484	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6958484	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6958484	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6958484	GS1-124K5.4	cis	Stomach	GTEx
rs6958484	RP4-756H11.3	cis	Thyroid	GTEx
rs6958484	GS1-124K5.11	cis	Thyroid	GTEx
rs6958484	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6958484	RP4-756H11.3	cis	lung	GTEx
rs6958484	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6958484	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6958484	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6958484	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65580600-65600600	Weak transcription	Aorta	Aorta
2	chr7:65580800-65606800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:65581600-65604800	Weak transcription	Colonic Mucosa	Colon
5	chr7:65582400-65608200	Weak transcription	Fetal Brain Male	brain
6	chr7:65585400-65604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:65587800-65606600	Weak transcription	Stomach Mucosa	stomach
8	chr7:65589800-65599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:65590800-65613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:65591600-65599800	Weak transcription	HSMMtube	muscle
11	chr7:65591600-65607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:65594000-65603400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:65594600-65604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:65594600-65604000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:65594600-65610800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:65594800-65606200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr7:65594800-65612200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:65594800-65614400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:65595000-65604000	Weak transcription	HUVEC	blood vessel
20	chr7:65595000-65614400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr7:65595000-65614600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:65595000-65615200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:65595200-65600600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:65595200-65602000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:65595200-65602200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:65595200-65602400	Strong transcription	Fetal Intestine Large	intestine
27	chr7:65595200-65605000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr7:65595200-65606200	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:65595200-65613600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:65595200-65614000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:65595200-65622000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:65595400-65599600	Strong transcription	Liver	Liver
33	chr7:65595400-65603600	Strong transcription	Fetal Thymus	thymus
34	chr7:65595600-65600400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:65595600-65600400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:65595600-65603400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:65595600-65623200	Strong transcription	Dnd41	blood
38	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
39	chr7:65595800-65599800	Strong transcription	GM12878-XiMat	blood
40	chr7:65595800-65601400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr7:65595800-65603400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:65595800-65603600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:65595800-65605600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:65595800-65608200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:65595800-65617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr7:65595800-65620000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:65596000-65599800	Strong transcription	Left Ventricle	heart
48	chr7:65596200-65600600	Strong transcription	NHDF-Ad	bronchial
49	chr7:65596200-65601800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:65596200-65602600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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