Variant report

Variant	rs4623294
Chromosome Location	chr7:65799471-65799472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1000464	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10224872	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10228885	0.82[EUR][1000 genomes]
rs10240949	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10250544	0.81[EUR][1000 genomes]
rs10255397	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10256544	0.83[EUR][1000 genomes]
rs10260426	0.82[EUR][1000 genomes]
rs10261398	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10263690	0.82[EUR][1000 genomes]
rs10276077	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10282433	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10447522	0.82[EUR][1000 genomes]
rs10807703	0.89[ASN][1000 genomes]
rs10950033	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11760844	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11769079	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11984115	0.82[EUR][1000 genomes]
rs12531677	0.82[EUR][1000 genomes]
rs12537823	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13230545	0.82[EUR][1000 genomes]
rs13309935	0.82[EUR][1000 genomes]
rs1532571	0.82[EUR][1000 genomes]
rs1643375	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1875057	0.82[EUR][1000 genomes]
rs2036263	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2036264	0.82[AFR][1000 genomes]
rs2088653	0.83[EUR][1000 genomes]
rs2088655	0.83[EUR][1000 genomes]
rs2901152	0.82[EUR][1000 genomes]
rs2901155	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909688	0.81[EUR][1000 genomes]
rs4078376	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4149461	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4236208	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4587224	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718328	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4718330	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6460284	0.82[EUR][1000 genomes]
rs6460287	0.82[EUR][1000 genomes]
rs6460290	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460293	0.83[EUR][1000 genomes]
rs6951503	0.82[EUR][1000 genomes]
rs6958294	0.82[EUR][1000 genomes]
rs6959268	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6960446	0.82[EUR][1000 genomes]
rs6962717	0.81[AMR][1000 genomes]
rs6971752	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6974614	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6976714	0.80[AMR][1000 genomes]
rs6979452	0.84[EUR][1000 genomes]
rs709596	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71526537	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7781880	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7782704	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7783613	0.82[AFR][1000 genomes]
rs7783779	0.82[EUR][1000 genomes]
rs778680	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778684	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778686	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778702	0.83[ASN][1000 genomes]
rs778715	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778716	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778719	0.82[ASN][1000 genomes]
rs778720	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778724	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778728	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778734	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778736	0.83[EUR][1000 genomes]
rs7796162	0.81[EUR][1000 genomes]
rs7798630	0.82[EUR][1000 genomes]
rs809025	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs880166	0.82[EUR][1000 genomes]
rs949930	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4623294	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs4623294	GTF2IRD1P1	cis	Thyroid	GTEx
rs4623294	GS1-124K5.4	cis	Stomach	GTEx
rs4623294	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4623294	LINC00174	cis	Thyroid	GTEx
rs4623294	RNU6-96P	cis	Thyroid	GTEx
rs4623294	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs4623294	RP4-756H11.3	cis	lung	GTEx
rs4623294	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs4623294	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs4623294	GS1-124K5.11	cis	Thyroid	GTEx
rs4623294	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs4623294	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4623294	RP4-756H11.3	cis	Artery Tibial	GTEx
rs4623294	RP4-756H11.3	cis	Thyroid	GTEx
rs4623294	RP4-756H11.3	cis	Artery Aorta	GTEx
rs4623294	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs4623294	GS1-124K5.4	cis	Whole Blood	GTEx
rs4623294	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65791800-65799600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:65791800-65800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:65792600-65799800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:65793000-65800200	Weak transcription	HSMM	muscle
5	chr7:65796200-65799800	Weak transcription	Pancreas	Pancrea
6	chr7:65796200-65801600	Weak transcription	Left Ventricle	heart
7	chr7:65796200-65809000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:65796400-65800000	Weak transcription	Fetal Stomach	stomach
9	chr7:65796400-65800400	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:65796800-65800200	Weak transcription	NHLF	lung
11	chr7:65796800-65809200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:65797200-65811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:65797800-65800000	Enhancers	HepG2	liver
14	chr7:65798200-65809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:65798800-65800200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:65799200-65800000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:65799200-65801400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:65799200-65801400	Weak transcription	Fetal Kidney	kidney

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