Variant report

Variant	rs11717923
Chromosome Location	chr3:158077527-158077528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10470472	0.89[ASN][1000 genomes]
rs10936131	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936139	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10936143	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10936144	0.80[AMR][1000 genomes]
rs10936145	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11707386	0.92[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11710813	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11712563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11715599	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11716327	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11716969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11717618	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11719124	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719153	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193511	1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1193513	0.91[ASN][1000 genomes]
rs1204957	0.81[ASN][1000 genomes]
rs1204960	0.80[ASN][1000 genomes]
rs12053861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12053865	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12053869	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493128	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12496934	0.92[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12631704	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12634807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634832	0.87[ASN][1000 genomes]
rs12636733	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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];0.96[ASN][1000 genomes]
rs12639310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059066	0.83[CHB][hapmap]
rs1729998	0.83[CHB][hapmap]
rs1730008	0.91[ASN][1000 genomes]
rs1730032	0.83[CHB][hapmap]
rs1730039	0.91[ASN][1000 genomes]
rs1730041	0.91[ASN][1000 genomes]
rs17627933	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17683939	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1851062	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1918000	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2139696	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682402	0.81[ASN][1000 genomes]
rs2693540	0.81[ASN][1000 genomes]
rs2693546	0.83[CHB][hapmap]
rs34434866	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4402974	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4680421	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs4680425	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4680435	0.92[CEU][hapmap];1.00[YRI][hapmap];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];1.00[ASN][1000 genomes]
rs58925169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60962704	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6441193	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767494	1.00[CEU][hapmap];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];1.00[ASN][1000 genomes]
rs6784968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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];0.96[ASN][1000 genomes]
rs6806967	1.00[YRI][hapmap];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];0.96[ASN][1000 genomes]
rs696715	0.83[CHB][hapmap]
rs698975	0.83[CHB][hapmap]
rs698976	0.83[CHB][hapmap]
rs698982	0.83[CHB][hapmap]
rs698992	0.82[CHB][hapmap]
rs699918	0.83[CHB][hapmap]
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];0.82[ASN][1000 genomes]
rs73168723	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73168799	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170303	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170331	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73170337	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170346	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73170364	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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];0.86[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];0.90[ASN][1000 genomes]
rs7641036	1.00[CEU][hapmap];1.00[YRI][hapmap];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]
rs827104	0.82[CHB][hapmap]
rs827130	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs827139	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs827141	0.82[CHB][hapmap]
rs827142	0.83[CHB][hapmap]
rs827153	0.83[CHB][hapmap]
rs827155	0.83[CHB][hapmap]
rs827160	0.83[CHB][hapmap]
rs827162	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs827168	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs827170	0.83[CHB][hapmap]
rs827173	0.82[CHB][hapmap]
rs827801	0.83[CHB][hapmap]
rs827805	0.83[CHB][hapmap]
rs862352	0.83[CHB][hapmap]
rs864331	0.83[CHB][hapmap]
rs866657	0.83[CHB][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11717923	RP11-538P18.2	cis	lung	GTEx
rs11717923	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11717923	RP11-538P18.2	cis	Artery Tibial	GTEx
rs11717923	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158047800-158077800	Weak transcription	Gastric	stomach
2	chr3:158048200-158079400	Weak transcription	Right Ventricle	heart
3	chr3:158055200-158086000	Weak transcription	Left Ventricle	heart
4	chr3:158057800-158079600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:158073600-158079400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:158075600-158077600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:158075800-158078400	Weak transcription	Esophagus	oesophagus
8	chr3:158076000-158077800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:158076200-158078600	ZNF genes & repeats	Dnd41	blood
10	chr3:158076200-158087000	Weak transcription	Aorta	Aorta
11	chr3:158076400-158078600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:158076400-158079800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:158076600-158078800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:158076600-158079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:158076800-158078800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:158076800-158079200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:158077000-158079200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:158077200-158078000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:158077200-158078000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr3:158077200-158078000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:158077200-158078200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
22	chr3:158077200-158078200	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr3:158077200-158078400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr3:158077200-158078400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:158077200-158078400	ZNF genes & repeats	Lung	lung
26	chr3:158077200-158078400	ZNF genes & repeats	Ovary	ovary
27	chr3:158077200-158078400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr3:158077200-158078600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:158077200-158078600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr3:158077200-158078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:158077200-158078600	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr3:158077200-158078800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
33	chr3:158077200-158079400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:158077400-158078000	ZNF genes & repeats	Fetal Muscle Leg	muscle
35	chr3:158077400-158078200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:158077400-158078200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr3:158077400-158078200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:158077400-158078400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
39	chr3:158077400-158078400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:158077400-158078400	Strong transcription	Adipose Nuclei	Adipose
41	chr3:158077400-158078600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:158077400-158078600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:158077400-158078600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr3:158077400-158078800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:158077400-158078800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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