Variant report

Variant	rs73170339
Chromosome Location	chr3:158078826-158078827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10470472	0.92[ASN][1000 genomes]
rs10936131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10936132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936139	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10936143	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10936144	0.80[AMR][1000 genomes]
rs10936145	0.80[AMR][1000 genomes]
rs1095636	0.82[ASN][1000 genomes]
rs11707386	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715599	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11716969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11717618	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11717923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719124	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719153	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1193511	0.95[ASN][1000 genomes]
rs1193513	0.95[ASN][1000 genomes]
rs1204957	0.84[ASN][1000 genomes]
rs1204960	0.83[ASN][1000 genomes]
rs12053861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053865	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12053869	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493128	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12496934	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12631704	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12634807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634832	0.90[ASN][1000 genomes]
rs12636733	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12637649	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12639261	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724679	0.82[ASN][1000 genomes]
rs1730008	0.95[ASN][1000 genomes]
rs1730039	0.95[ASN][1000 genomes]
rs1730041	0.95[ASN][1000 genomes]
rs17627933	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17683939	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1851062	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1918000	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2139696	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682402	0.84[ASN][1000 genomes]
rs2693540	0.84[ASN][1000 genomes]
rs34434866	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680421	0.91[EUR][1000 genomes]
rs4680425	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4680435	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56123505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58195752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58925169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60962704	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6441193	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767494	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6772246	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784968	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800218	0.84[EUR][1000 genomes]
rs6800853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806967	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6807468	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698992	0.82[ASN][1000 genomes]
rs699918	0.82[ASN][1000 genomes]
rs73164102	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73166358	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73168723	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73168799	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73170303	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73170306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73170310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170331	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73170337	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170346	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170364	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170373	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73170375	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73172105	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73172114	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73172119	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7640075	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7652970	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs827130	0.92[ASN][1000 genomes]
rs827139	0.84[ASN][1000 genomes]
rs827162	0.92[ASN][1000 genomes]
rs827168	0.92[ASN][1000 genomes]
rs827170	0.82[ASN][1000 genomes]
rs827173	0.80[ASN][1000 genomes]
rs827174	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73170339	RP11-538P18.2	cis	Artery Tibial	GTEx
rs73170339	RP11-538P18.2	cis	lung	GTEx
rs73170339	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158048200-158079400	Weak transcription	Right Ventricle	heart
2	chr3:158055200-158086000	Weak transcription	Left Ventricle	heart
3	chr3:158057800-158079600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:158073600-158079400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:158076200-158087000	Weak transcription	Aorta	Aorta
6	chr3:158076400-158079800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:158076600-158079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:158076800-158079200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:158077000-158079200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:158077200-158079400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:158077600-158079200	ZNF genes & repeats	Spleen	Spleen
12	chr3:158077800-158079000	ZNF genes & repeats	Fetal Stomach	stomach
13	chr3:158077800-158079400	Weak transcription	Primary T cells from cord blood	blood
14	chr3:158078000-158079600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:158078200-158079200	Strong transcription	Primary B cells from cord blood	blood
16	chr3:158078200-158079800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:158078200-158081200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:158078400-158079200	ZNF genes & repeats	Esophagus	oesophagus
19	chr3:158078400-158080000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:158078400-158080600	Weak transcription	Gastric	stomach
21	chr3:158078600-158079000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:158078600-158080200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:158078600-158080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:158078600-158082800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:158078600-158084600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:158078800-158079200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:158078800-158080400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:158078800-158080800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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