Variant report

Variant	rs12631513
Chromosome Location	chr3:101517476-101517477
allele	A/C
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:60)

rs_ID	r²[population]
rs1031710	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706494	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706986	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707250	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712888	0.97[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	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716558	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717046	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717638	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720745	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11914318	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919389	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12633089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633770	0.92[AFR][1000 genomes];0.85[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	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13068350	0.85[EUR][1000 genomes]
rs13077925	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13078652	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084113	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084432	0.84[EUR][1000 genomes]
rs13085776	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099674	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1460097	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347156	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17347644	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963961	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963962	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34063583	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34161138	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181125	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34263427	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34376498	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34648996	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743741	0.87[AFR][1000 genomes];0.98[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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34963630	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35117343	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35315807	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35799195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35810977	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35850993	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36002990	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4342086	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55859364	0.81[ASN][1000 genomes]
rs58658478	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61396602	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284198	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62284199	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830943	0.81[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	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
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12631513	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 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	chr3:101499000-101523000	Weak transcription	Stomach Mucosa	stomach
5	chr3:101499000-101533000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:101499200-101529600	Weak transcription	Small Intestine	intestine
7	chr3:101499800-101524800	Weak transcription	HepG2	liver
8	chr3:101502600-101540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:101502600-101540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:101502800-101528200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:101503200-101522400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:101504600-101520200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:101504600-101524400	Weak transcription	Gastric	stomach
14	chr3:101504800-101533600	Weak transcription	Pancreas	Pancrea
15	chr3:101504800-101546000	Weak transcription	Colonic Mucosa	Colon
16	chr3:101505000-101520000	Weak transcription	Right Ventricle	heart
17	chr3:101505400-101533600	Weak transcription	Right Atrium	heart
18	chr3:101509800-101520000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:101509800-101528200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:101510000-101522400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:101510200-101522400	Weak transcription	Fetal Brain Male	brain
22	chr3:101510200-101525600	Weak transcription	Placenta	Placenta
23	chr3:101511000-101518600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:101511000-101521800	Weak transcription	Fetal Kidney	kidney
25	chr3:101511000-101527200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:101511000-101536000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:101511400-101520000	Weak transcription	Psoas Muscle	Psoas
28	chr3:101512000-101519600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:101512000-101521800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:101513000-101528000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:101513600-101519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:101513600-101519800	Weak transcription	Fetal Brain Female	brain
33	chr3:101514200-101520200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:101515000-101520000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:101515200-101517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:101515200-101517800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:101515200-101518800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:101515200-101519600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:101515200-101519800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:101515200-101520000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:101515200-101520000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:101515200-101520000	Weak transcription	Fetal Lung	lung
43	chr3:101515200-101520200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:101515200-101520200	Weak transcription	Lung	lung
45	chr3:101515200-101522200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:101515200-101522800	Weak transcription	NHDF-Ad	bronchial
47	chr3:101515200-101528200	Weak transcription	NH-A	brain
48	chr3:101515200-101540200	Weak transcription	NHLF	lung
49	chr3:101515400-101517600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:101515400-101519800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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