Variant report

Variant	rs62466793
Chromosome Location	chr7:66191517-66191518
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	chr7:66189119..66192033-chr7:66195349..66197808,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10215132	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10215516	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10234018	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10249404	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10252765	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10255377	0.82[EUR][1000 genomes]
rs10263935	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10272357	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10272546	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10274773	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10278371	0.89[EUR][1000 genomes]
rs10278816	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281080	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281646	0.81[AFR][1000 genomes]
rs10950044	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1110414	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765356	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11766262	0.86[EUR][1000 genomes]
rs11768727	0.97[EUR][1000 genomes]
rs11772264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11772636	0.96[EUR][1000 genomes]
rs11773829	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13227951	0.87[EUR][1000 genomes]
rs13239306	0.81[EUR][1000 genomes]
rs1553609	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553610	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17566701	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860468	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1860470	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1961155	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1968127	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2003301	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2013222	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2055682	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2191268	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286683	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286684	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2420824	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2420827	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659889	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659899	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659906	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659909	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659912	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659915	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2659916	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707822	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2707827	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2707836	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707841	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707845	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2707848	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707849	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707850	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707852	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707853	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707854	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707856	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28698552	0.82[EUR][1000 genomes]
rs28830215	0.89[EUR][1000 genomes]
rs28887326	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3069894	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34356500	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35130766	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35526611	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35986979	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764903	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800812	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800820	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800823	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857686	0.89[EUR][1000 genomes]
rs3857688	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3898855	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4273746	0.82[EUR][1000 genomes]
rs4279493	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717310	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717319	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718403	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718405	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56229325	0.86[EUR][1000 genomes]
rs62465434	0.82[EUR][1000 genomes]
rs62466794	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467857	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460305	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460308	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460309	0.81[EUR][1000 genomes]
rs6943696	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6949912	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958520	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6960778	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6965056	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6979488	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71563125	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7357230	0.86[EUR][1000 genomes]
rs7779971	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782320	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7783924	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7785213	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7788576	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789184	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7789419	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7793569	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7807930	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7807944	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs801190	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801193	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801196	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs801205	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801211	0.83[EUR][1000 genomes]
rs801216	0.81[EUR][1000 genomes]
rs801217	0.82[EUR][1000 genomes]
rs810400	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9791890	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs62466793	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs62466793	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs62466793	RP4-756H11.3	cis	Stomach	GTEx
rs62466793	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs62466793	RP4-756H11.3	cis	lung	GTEx
rs62466793	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs62466793	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs62466793	RP4-756H11.3	cis	Artery Aorta	GTEx
rs62466793	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs62466793	RP4-756H11.3	cis	Artery Tibial	GTEx
rs62466793	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs62466793	RP4-756H11.3	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
2	chr7:66162600-66192400	Weak transcription	NH-A	brain
3	chr7:66162600-66196800	Weak transcription	Right Ventricle	heart
4	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:66165800-66197000	Weak transcription	Right Atrium	heart
6	chr7:66176400-66204600	Weak transcription	Colonic Mucosa	Colon
7	chr7:66177600-66193600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:66178600-66200400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:66178800-66193600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:66178800-66197000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:66179000-66197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:66179200-66200600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:66179400-66199800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:66179600-66204600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:66180800-66193600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:66181600-66193600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:66181600-66196000	Weak transcription	Ovary	ovary
18	chr7:66181600-66202000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:66182600-66199800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:66182800-66205000	Weak transcription	Gastric	stomach
21	chr7:66184000-66192200	Weak transcription	Fetal Brain Female	brain
22	chr7:66184400-66192200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:66185400-66197600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:66185800-66191600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:66188200-66191800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:66188400-66196800	Weak transcription	Adipose Nuclei	Adipose
27	chr7:66188400-66201800	Weak transcription	Fetal Brain Male	brain
28	chr7:66189400-66191600	Strong transcription	NHDF-Ad	bronchial
29	chr7:66189400-66197000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:66189600-66191800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:66189600-66193600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:66189800-66191600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:66189800-66196800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:66190000-66193800	Strong transcription	Fetal Intestine Small	intestine
35	chr7:66190000-66194000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:66190000-66200400	Weak transcription	HepG2	liver
37	chr7:66190000-66201200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:66190200-66191600	Strong transcription	Fetal Intestine Large	intestine
39	chr7:66190200-66198800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:66190400-66191600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:66190400-66191600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:66190400-66191600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:66190400-66196200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:66190400-66197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr7:66190400-66204600	Weak transcription	Stomach Mucosa	stomach
46	chr7:66190600-66191600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:66190600-66191600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:66190600-66191800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:66190600-66192000	Strong transcription	Fetal Muscle Leg	muscle
50	chr7:66190600-66193600	Strong transcription	Fetal Stomach	stomach

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