Variant report

Variant	rs11764589
Chromosome Location	chr7:65897040-65897041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1000464	0.83[EUR][1000 genomes]
rs10224872	0.85[EUR][1000 genomes]
rs10228885	0.81[EUR][1000 genomes]
rs10240949	0.87[EUR][1000 genomes]
rs10250544	0.81[EUR][1000 genomes]
rs10255397	0.83[EUR][1000 genomes]
rs10256544	0.81[EUR][1000 genomes]
rs10260426	0.82[EUR][1000 genomes]
rs10261398	0.85[EUR][1000 genomes]
rs10263690	0.82[EUR][1000 genomes]
rs10276077	0.85[EUR][1000 genomes]
rs10282433	0.86[EUR][1000 genomes]
rs10447522	0.82[EUR][1000 genomes]
rs10807704	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1083554	0.87[EUR][1000 genomes]
rs10950033	0.86[EUR][1000 genomes]
rs11760844	0.86[EUR][1000 genomes]
rs11763189	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11765791	0.85[EUR][1000 genomes]
rs11769079	0.87[EUR][1000 genomes]
rs11773628	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11984115	0.81[EUR][1000 genomes]
rs12531677	0.82[EUR][1000 genomes]
rs12537823	0.86[EUR][1000 genomes]
rs12668005	0.86[EUR][1000 genomes]
rs12698522	0.82[EUR][1000 genomes]
rs12698526	0.83[EUR][1000 genomes]
rs13230545	0.82[EUR][1000 genomes]
rs13309935	0.80[EUR][1000 genomes]
rs1532571	0.82[EUR][1000 genomes]
rs1643375	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1695820	0.83[EUR][1000 genomes]
rs1875057	0.82[EUR][1000 genomes]
rs2036263	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088653	0.83[EUR][1000 genomes]
rs2088655	0.82[EUR][1000 genomes]
rs2420608	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28714531	0.83[EUR][1000 genomes]
rs2901152	0.81[EUR][1000 genomes]
rs2901209	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2909688	0.85[EUR][1000 genomes]
rs3857685	0.85[EUR][1000 genomes]
rs4078376	0.86[EUR][1000 genomes]
rs4149461	0.86[EUR][1000 genomes]
rs4236208	0.86[EUR][1000 genomes]
rs4587224	0.86[EUR][1000 genomes]
rs4718328	0.82[EUR][1000 genomes]
rs4718330	0.84[EUR][1000 genomes]
rs4718356	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57739047	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460284	0.82[EUR][1000 genomes]
rs6460287	0.81[EUR][1000 genomes]
rs6460290	0.87[EUR][1000 genomes]
rs6460293	0.83[EUR][1000 genomes]
rs6460301	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460302	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460303	0.83[EUR][1000 genomes]
rs6460304	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6945775	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6951503	0.82[EUR][1000 genomes]
rs6958294	0.82[EUR][1000 genomes]
rs6959268	0.85[EUR][1000 genomes]
rs6960446	0.82[EUR][1000 genomes]
rs6962717	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6963228	0.88[EUR][1000 genomes]
rs6971752	0.85[EUR][1000 genomes]
rs6976714	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6978028	0.89[EUR][1000 genomes]
rs6979452	0.82[EUR][1000 genomes]
rs6980451	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs709596	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7778322	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7782704	0.87[EUR][1000 genomes]
rs7783779	0.82[EUR][1000 genomes]
rs778680	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778684	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778686	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778690	0.89[EUR][1000 genomes]
rs778697	0.89[EUR][1000 genomes]
rs778702	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778703	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778705	0.88[EUR][1000 genomes]
rs778707	0.88[EUR][1000 genomes]
rs778711	0.86[EUR][1000 genomes]
rs778715	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778716	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778719	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778720	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778724	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778728	0.84[EUR][1000 genomes]
rs778734	0.87[EUR][1000 genomes]
rs778736	0.83[EUR][1000 genomes]
rs7789615	0.87[EUR][1000 genomes]
rs7796162	0.80[EUR][1000 genomes]
rs7798630	0.82[EUR][1000 genomes]
rs809025	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs880166	0.80[EUR][1000 genomes]
rs949930	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv970867	chr7:65893874-65900243	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11764589	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs11764589	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11764589	LINC00174	cis	Thyroid	GTEx
rs11764589	RP4-756H11.3	cis	lung	GTEx
rs11764589	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11764589	GS1-124K5.11	cis	Thyroid	GTEx
rs11764589	GTF2IRD1P1	cis	Thyroid	GTEx
rs11764589	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs11764589	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs11764589	RP4-756H11.3	cis	Thyroid	GTEx
rs11764589	RP4-756H11.3	cis	Artery Tibial	GTEx
rs11764589	GS1-124K5.2	cis	Whole Blood	GTEx
rs11764589	RNU6-96P	cis	Thyroid	GTEx
rs11764589	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs11764589	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs11764589	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65905600	Weak transcription	Lung	lung
2	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
4	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
5	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
6	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
7	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
8	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:65879200-65946000	Weak transcription	NHEK	skin
10	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
11	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
13	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
16	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
17	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
20	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:65879600-65900600	Weak transcription	Brain Germinal Matrix	brain
22	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
26	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:65884000-65919600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:65885000-65904200	Weak transcription	K562	blood
29	chr7:65886000-65913600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:65886600-65920400	Weak transcription	Right Ventricle	heart
31	chr7:65887000-65924600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:65887000-65924600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:65887200-65904600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:65889000-65898200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:65889200-65903000	Weak transcription	Thymus	Thymus
36	chr7:65889200-65939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:65889600-65913800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:65890000-65928800	Weak transcription	Adipose Nuclei	Adipose
39	chr7:65890200-65907400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:65890400-65916200	Weak transcription	Fetal Thymus	thymus
41	chr7:65891400-65902000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:65891600-65939000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:65892000-65931800	Weak transcription	Ovary	ovary
44	chr7:65893200-65913400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:65894200-65899800	Weak transcription	Spleen	Spleen
46	chr7:65894200-65905400	Weak transcription	Gastric	stomach
47	chr7:65894200-65939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:65894600-65899400	Weak transcription	Fetal Muscle Leg	muscle
49	chr7:65894600-65905200	Weak transcription	Pancreas	Pancrea
50	chr7:65894800-65897200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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