Variant report

Variant	rs6952473
Chromosome Location	chr7:65696853-65696854
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	chr7:65692053..65693924-chr7:65696196..65697706,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1000464	0.85[EUR][1000 genomes]
rs10224872	0.87[EUR][1000 genomes]
rs10228885	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10240949	0.86[EUR][1000 genomes]
rs10250544	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10255397	0.84[EUR][1000 genomes]
rs10256544	0.90[EUR][1000 genomes]
rs10257911	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10260426	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10261398	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10263690	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10272149	0.84[EUR][1000 genomes]
rs10276077	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10282433	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10447522	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1083554	0.85[EUR][1000 genomes]
rs10950033	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11760844	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11769079	0.83[EUR][1000 genomes]
rs11984115	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12531677	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12534500	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537823	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13225672	0.81[EUR][1000 genomes]
rs13230545	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13309935	0.89[EUR][1000 genomes]
rs1532571	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1875057	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036263	0.86[EUR][1000 genomes]
rs2088653	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2088655	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2420173	0.81[EUR][1000 genomes]
rs2420174	0.81[EUR][1000 genomes]
rs28391294	0.82[EUR][1000 genomes]
rs28491091	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2901152	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909688	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34913718	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3893216	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4078376	0.87[EUR][1000 genomes]
rs4149461	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4236208	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4587224	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4718319	0.81[EUR][1000 genomes]
rs4718324	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718328	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718329	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718330	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6460278	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460279	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460282	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460284	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460287	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6460290	0.86[EUR][1000 genomes]
rs6460293	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6944374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951503	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6952182	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6958294	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6959268	0.86[EUR][1000 genomes]
rs6960446	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6963228	0.83[EUR][1000 genomes]
rs6964437	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6967708	0.81[EUR][1000 genomes]
rs6971752	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6974614	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6978028	0.83[EUR][1000 genomes]
rs6979452	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs709596	0.86[EUR][1000 genomes]
rs7781880	0.83[EUR][1000 genomes]
rs7782704	0.86[EUR][1000 genomes]
rs7782806	0.81[EUR][1000 genomes]
rs7783779	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778680	0.85[EUR][1000 genomes]
rs778684	0.86[EUR][1000 genomes]
rs778686	0.86[EUR][1000 genomes]
rs778690	0.83[EUR][1000 genomes]
rs778697	0.83[EUR][1000 genomes]
rs778705	0.84[EUR][1000 genomes]
rs778707	0.84[EUR][1000 genomes]
rs778711	0.84[EUR][1000 genomes]
rs778715	0.80[EUR][1000 genomes]
rs778716	0.80[EUR][1000 genomes]
rs778720	0.80[EUR][1000 genomes]
rs778724	0.86[EUR][1000 genomes]
rs778728	0.83[EUR][1000 genomes]
rs778734	0.86[EUR][1000 genomes]
rs778736	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7787482	0.85[EUR][1000 genomes]
rs7789615	0.81[EUR][1000 genomes]
rs7796162	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7798630	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs809025	0.80[EUR][1000 genomes]
rs880166	0.89[EUR][1000 genomes]
rs949930	0.87[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	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	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6952473	LINC00174	cis	Thyroid	GTEx
rs6952473	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6952473	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6952473	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6952473	GS1-124K5.11	cis	Thyroid	GTEx
rs6952473	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6952473	RP4-756H11.3	cis	lung	GTEx
rs6952473	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6952473	RP4-756H11.3	cis	Whole Blood	GTEx
rs6952473	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6952473	RNU6-96P	cis	Thyroid	GTEx
rs6952473	GTF2IRD1P1	cis	Thyroid	GTEx
rs6952473	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6952473	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6952473	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6952473	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6952473	GS1-124K5.4	cis	Stomach	GTEx
rs6952473	RP4-756H11.3	cis	Thyroid	GTEx
rs6952473	GS1-124K5.4	cis	Artery Aorta	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
3	chr7:65686800-65701600	Weak transcription	Osteobl	bone
4	chr7:65686800-65715400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:65687000-65701800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:65687000-65701800	Weak transcription	NHDF-Ad	bronchial
7	chr7:65687800-65701800	Weak transcription	Spleen	Spleen
8	chr7:65687800-65703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:65689400-65703600	Weak transcription	NHLF	lung
10	chr7:65689600-65697800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:65689600-65701800	Weak transcription	Gastric	stomach
12	chr7:65689600-65715800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:65689800-65697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:65689800-65701800	Weak transcription	Fetal Lung	lung
15	chr7:65689800-65701800	Weak transcription	HMEC	breast
16	chr7:65689800-65702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:65690000-65698400	Weak transcription	Liver	Liver
18	chr7:65690200-65701800	Weak transcription	Ovary	ovary
19	chr7:65691200-65700200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:65694400-65698400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:65695800-65709400	Weak transcription	Psoas Muscle	Psoas
22	chr7:65696200-65697000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr7:65696200-65697000	ZNF genes & repeats	Fetal Stomach	stomach
24	chr7:65696200-65697400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:65696200-65697800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:65696400-65697000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:65696400-65698600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:65696600-65698600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:65696600-65701800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:65696600-65701800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:65696600-65702000	Weak transcription	Lung	lung
32	chr7:65696800-65698000	Weak transcription	Esophagus	oesophagus
33	chr7:65696800-65698800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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