Variant report

Variant	rs880166
Chromosome Location	chr7:65670762-65670763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs1000464	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1002053	0.85[CEU][hapmap]
rs10215948	0.89[CEU][hapmap]
rs10224872	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10228885	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs10240249	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10240949	0.93[EUR][1000 genomes]
rs10250544	0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs10253922	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10255397	0.89[EUR][1000 genomes]
rs10256544	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10257427	0.89[CEU][hapmap]
rs10257911	0.89[EUR][1000 genomes]
rs10260426	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes]
rs10261398	1.00[CEU][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10263690	0.91[EUR][1000 genomes]
rs10267430	0.89[CEU][hapmap]
rs10268656	0.81[AMR][1000 genomes]
rs10271553	0.84[AMR][1000 genomes]
rs10272149	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10276077	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10282433	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10447522	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes]
rs1083554	0.83[EUR][1000 genomes]
rs10950033	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1129531	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1167390	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1167406	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs11760844	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11764589	0.80[EUR][1000 genomes]
rs11765965	0.83[CEU][hapmap]
rs11769079	0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs1183245	0.89[CEU][hapmap]
rs11974219	0.82[AMR][1000 genomes]
rs11974264	0.83[AMR][1000 genomes]
rs11984115	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs12531677	0.91[EUR][1000 genomes]
rs12534500	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12537823	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13225383	0.80[AMR][1000 genomes]
rs13225672	0.89[EUR][1000 genomes]
rs13230545	0.91[EUR][1000 genomes]
rs13245728	1.00[YRI][hapmap]
rs13309935	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532571	0.91[EUR][1000 genomes]
rs1540651	0.81[AMR][1000 genomes]
rs1565531	0.84[AMR][1000 genomes]
rs1612452	0.83[AMR][1000 genomes]
rs1616988	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes]
rs1643375	0.83[EUR][1000 genomes]
rs1695820	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs1875057	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes]
rs1976200	1.00[YRI][hapmap]
rs1983372	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2036263	0.93[EUR][1000 genomes]
rs2036264	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs2087647	0.93[CEU][hapmap]
rs2088653	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs2088655	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[EUR][1000 genomes]
rs2173570	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs2220626	0.93[CEU][hapmap]
rs2249458	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2420173	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420174	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460432	0.81[AMR][1000 genomes]
rs28391294	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28470208	0.85[AMR][1000 genomes]
rs28491091	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2901152	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs2909688	0.87[EUR][1000 genomes]
rs313829	0.82[YRI][hapmap]
rs34913718	0.89[EUR][1000 genomes]
rs35028832	0.84[AMR][1000 genomes]
rs35034167	0.85[AMR][1000 genomes]
rs3893216	0.87[EUR][1000 genomes]
rs4078376	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4149461	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236208	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4368860	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4587224	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4612218	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4623294	0.82[EUR][1000 genomes]
rs4718319	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718324	0.90[EUR][1000 genomes]
rs4718328	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718329	0.88[EUR][1000 genomes]
rs4718330	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57866200	0.84[AMR][1000 genomes]
rs59466412	0.84[AMR][1000 genomes]
rs6460278	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6460279	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6460282	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6460284	0.91[EUR][1000 genomes]
rs6460287	0.90[EUR][1000 genomes]
rs6460290	0.93[EUR][1000 genomes]
rs6460292	0.89[CEU][hapmap]
rs6460293	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs6944374	0.96[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6945843	0.92[CEU][hapmap]
rs6946143	0.89[CEU][hapmap]
rs6951503	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6951787	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6952182	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6952473	0.89[EUR][1000 genomes]
rs6956179	0.89[CEU][hapmap]
rs6958294	0.91[EUR][1000 genomes]
rs6958484	0.88[CEU][hapmap]
rs6959268	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs6960446	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes]
rs6961717	0.89[CEU][hapmap]
rs6962717	0.83[EUR][1000 genomes]
rs6963228	0.81[EUR][1000 genomes]
rs6963646	0.89[CEU][hapmap]
rs6964437	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6967708	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971509	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6971752	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6974614	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6976714	0.82[EUR][1000 genomes]
rs6977501	0.86[AFR][1000 genomes]
rs6978028	0.81[EUR][1000 genomes]
rs6979452	0.89[EUR][1000 genomes]
rs697968	0.89[CEU][hapmap]
rs697970	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs709595	0.89[CEU][hapmap]
rs709596	0.92[EUR][1000 genomes]
rs709608	0.81[AMR][1000 genomes]
rs709609	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes]
rs71526537	0.82[EUR][1000 genomes]
rs7781880	0.85[EUR][1000 genomes]
rs7782704	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs7782806	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7783613	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs7783779	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes]
rs778680	0.92[EUR][1000 genomes]
rs778684	0.93[EUR][1000 genomes]
rs778686	0.93[EUR][1000 genomes]
rs7786892	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778690	0.81[EUR][1000 genomes]
rs778697	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs778702	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs778703	0.81[EUR][1000 genomes]
rs778705	0.82[EUR][1000 genomes]
rs778706	0.89[CEU][hapmap]
rs778707	0.82[EUR][1000 genomes]
rs778711	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs778715	0.86[EUR][1000 genomes]
rs778716	0.86[EUR][1000 genomes]
rs778719	0.80[EUR][1000 genomes]
rs778720	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs778722	0.92[CEU][hapmap]
rs778724	0.93[EUR][1000 genomes]
rs778728	0.90[EUR][1000 genomes]
rs778734	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs778736	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs7787482	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7794930	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs7796162	0.89[EUR][1000 genomes]
rs7798630	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs7801282	0.89[CEU][hapmap]
rs7809814	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs809025	0.85[EUR][1000 genomes]
rs875971	0.89[CEU][hapmap]
rs908915	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937495	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs949930	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][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	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
4	esv3375675	chr7:65669142-65671690	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs880166	RP4-756H11.3	cis	Artery Tibial	GTEx
rs880166	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs880166	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs880166	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs880166	RNU6-96P	cis	Thyroid	GTEx
rs880166	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs880166	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs880166	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs880166	GTF2IRD1P1	cis	Thyroid	GTEx
rs880166	RP4-756H11.3	cis	lung	GTEx
rs880166	GS1-124K5.2	cis	Whole Blood	GTEx
rs880166	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs880166	GS1-124K5.11	cis	Thyroid	GTEx
rs880166	LINC00174	cis	Thyroid	GTEx
rs880166	GS1-124K5.4	cis	Stomach	GTEx
rs880166	ENSG00000169902	cis	multi-tissue	Pritchard
rs880166	RP4-756H11.3	cis	Thyroid	GTEx
rs880166	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65669400-65670800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr7:65669400-65671000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr7:65669400-65671000	Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr7:65669400-65671000	Active TSS	Fetal Kidney	kidney
5	chr7:65669400-65671200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr7:65669400-65671200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:65669400-65672200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:65669400-65672400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:65669400-65673200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:65669600-65670800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr7:65669600-65670800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:65669600-65670800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr7:65669600-65670800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr7:65669600-65670800	Active TSS	Brain Substantia Nigra	brain
15	chr7:65669600-65671000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr7:65669600-65671000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:65669600-65671000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:65669600-65671000	Active TSS	Brain Angular Gyrus	brain
19	chr7:65669600-65671000	Active TSS	Colon Smooth Muscle	Colon
20	chr7:65669600-65671200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:65669600-65671200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:65669600-65671200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:65669600-65671200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr7:65669600-65671200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:65669600-65671200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr7:65669600-65671200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr7:65669600-65671200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:65669600-65671200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr7:65669600-65671200	Active TSS	Esophagus	oesophagus
30	chr7:65669600-65671200	Active TSS	Fetal Brain Female	brain
31	chr7:65669600-65671200	Active TSS	Fetal Lung	lung
32	chr7:65669600-65671200	Active TSS	Ovary	ovary
33	chr7:65669600-65671400	Active TSS	Primary T cells from cord blood	blood
34	chr7:65669600-65671400	Active TSS	Brain Anterior Caudate	brain
35	chr7:65669600-65671400	Active TSS	Brain Cingulate Gyrus	brain
36	chr7:65669600-65671400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr7:65669600-65671400	Active TSS	HSMM	muscle
38	chr7:65669600-65671600	Active TSS	Pancreas	Pancrea
39	chr7:65669600-65672200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr7:65669600-65672200	Active TSS	Right Atrium	heart
41	chr7:65669600-65672400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:65669600-65673000	Active TSS	NHDF-Ad	bronchial
43	chr7:65669800-65670800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr7:65669800-65670800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:65669800-65670800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:65669800-65670800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:65669800-65670800	Flanking Active TSS	Colonic Mucosa	Colon
48	chr7:65669800-65670800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr7:65669800-65670800	Active TSS	Fetal Stomach	stomach
50	chr7:65669800-65671000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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