Variant report

Variant	rs11717638
Chromosome Location	chr3:101505468-101505469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1031710	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706494	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706986	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712748	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11712888	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716558	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717046	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718446	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11720745	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11914318	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919389	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631513	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633770	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059470	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060963	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065944	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13066768	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13068350	0.85[EUR][1000 genomes]
rs13069443	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13077925	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13078652	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081846	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13084113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084432	0.84[EUR][1000 genomes]
rs13085776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094911	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099674	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1460097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17347644	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17411983	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1963961	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963962	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288272	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2290859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3094296	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3094297	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs34063583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34161138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181125	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34263427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34376498	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34648996	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743741	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34947019	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34963630	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35117343	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35315807	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35799195	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35810977	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35850993	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36002990	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762729	0.85[JPT][hapmap]
rs3804775	0.85[JPT][hapmap]
rs3806653	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3806654	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4342086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55859364	0.81[ASN][1000 genomes]
rs58658478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61396602	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284198	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62284199	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7629753	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7651721	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9830943	0.93[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs997739	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11717638	NXPE3	cis	Esophagus Muscularis	GTEx
rs11717638	FAM55C	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101498800-101508200	Weak transcription	Placenta	Placenta
2	chr3:101498800-101519000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:101498800-101533800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:101498800-101546200	Weak transcription	Esophagus	oesophagus
5	chr3:101499000-101513200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:101499000-101523000	Weak transcription	Stomach Mucosa	stomach
7	chr3:101499000-101533000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:101499200-101529600	Weak transcription	Small Intestine	intestine
9	chr3:101499400-101510600	Weak transcription	Fetal Kidney	kidney
10	chr3:101499800-101512200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:101499800-101524800	Weak transcription	HepG2	liver
12	chr3:101500000-101509400	Weak transcription	Fetal Intestine Small	intestine
13	chr3:101500400-101508000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:101500400-101508000	Weak transcription	GM12878-XiMat	blood
15	chr3:101500400-101511800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:101500600-101511000	Strong transcription	HSMM	muscle
17	chr3:101501200-101507000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:101501200-101507400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr3:101501200-101510800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:101501200-101511000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:101501200-101516200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:101501400-101506600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:101501400-101506600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:101501400-101507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:101501400-101507200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:101501400-101509600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:101501400-101511200	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:101501600-101506600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:101501600-101506600	Strong transcription	Fetal Stomach	stomach
30	chr3:101501600-101506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:101501600-101507200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:101501600-101507200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:101501600-101507200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr3:101501600-101510200	Strong transcription	Osteobl	bone
35	chr3:101501600-101511000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:101501600-101511000	Strong transcription	Fetal Brain Female	brain
37	chr3:101501600-101515000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:101501800-101506800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:101502000-101510600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:101502000-101510600	Strong transcription	Fetal Lung	lung
41	chr3:101502200-101505800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:101502200-101505800	Strong transcription	NH-A	brain
43	chr3:101502200-101505800	Strong transcription	NHDF-Ad	bronchial
44	chr3:101502200-101506000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:101502200-101506400	Strong transcription	Lung	lung
46	chr3:101502200-101506600	Strong transcription	HSMMtube	muscle
47	chr3:101502200-101506800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:101502200-101507200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:101502200-101507200	Strong transcription	Brain Germinal Matrix	brain
50	chr3:101502200-101507400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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