Variant report

Variant	rs13078652
Chromosome Location	chr3:101511153-101511154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1031710	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706494	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706986	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707250	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710805	0.80[EUR][1000 genomes]
rs11711903	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712309	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712888	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714444	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716558	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717046	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717638	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720745	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11914318	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919389	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631513	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633089	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633770	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059470	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060963	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065944	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13066768	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13068350	0.85[EUR][1000 genomes]
rs13077925	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084113	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084432	0.84[EUR][1000 genomes]
rs13085776	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094753	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094911	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099674	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1460097	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347156	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17347644	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963961	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963962	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290859	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34063583	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34161138	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181125	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34263427	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34376498	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34648996	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743741	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34947019	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34963630	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35117343	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35315807	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35799195	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35810977	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35850993	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36002990	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4342086	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55859364	0.81[ASN][1000 genomes]
rs58658478	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61396602	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284198	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62284199	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830943	0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13078652	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101498800-101519000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:101498800-101533800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:101498800-101546200	Weak transcription	Esophagus	oesophagus
4	chr3:101499000-101513200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:101499000-101523000	Weak transcription	Stomach Mucosa	stomach
6	chr3:101499000-101533000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:101499200-101529600	Weak transcription	Small Intestine	intestine
8	chr3:101499800-101512200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:101499800-101524800	Weak transcription	HepG2	liver
10	chr3:101500400-101511800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:101501200-101516200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:101501400-101511200	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:101501600-101515000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:101502200-101511200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:101502200-101511600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:101502200-101516000	Strong transcription	A549	lung
17	chr3:101502600-101540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:101502600-101540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:101502800-101528200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:101503200-101522400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:101504600-101512000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr3:101504600-101514800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:101504600-101520200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:101504600-101524400	Weak transcription	Gastric	stomach
25	chr3:101504800-101511400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:101504800-101511400	Strong transcription	Brain Anterior Caudate	brain
27	chr3:101504800-101515800	Strong transcription	Fetal Thymus	thymus
28	chr3:101504800-101533600	Weak transcription	Pancreas	Pancrea
29	chr3:101504800-101546000	Weak transcription	Colonic Mucosa	Colon
30	chr3:101505000-101512600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:101505000-101517400	Weak transcription	Fetal Heart	heart
32	chr3:101505000-101520000	Weak transcription	Right Ventricle	heart
33	chr3:101505200-101512200	Weak transcription	NHLF	lung
34	chr3:101505200-101514800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:101505400-101514600	Weak transcription	Spleen	Spleen
36	chr3:101505400-101533600	Weak transcription	Right Atrium	heart
37	chr3:101505600-101514800	Weak transcription	Adipose Nuclei	Adipose
38	chr3:101505800-101515600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:101506400-101512200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:101506400-101514600	Weak transcription	HUVEC	blood vessel
41	chr3:101506400-101514800	Weak transcription	Lung	lung
42	chr3:101506600-101512200	Weak transcription	HSMMtube	muscle
43	chr3:101507000-101511400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:101507000-101514600	Weak transcription	HMEC	breast
45	chr3:101507400-101513400	Strong transcription	Primary T cells from cord blood	blood
46	chr3:101507600-101511200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:101507800-101511600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:101508000-101511600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:101508000-101514000	ZNF genes & repeats	GM12878-XiMat	blood
50	chr3:101508000-101515400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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