Variant report

Variant	rs13077925
Chromosome Location	chr3:101488181-101488182
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1031710	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1056579	0.89[ASN][1000 genomes]
rs1138818	0.92[ASN][1000 genomes]
rs11706494	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706986	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707250	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710805	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711079	0.91[ASN][1000 genomes]
rs11711903	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	0.91[ASN][1000 genomes]
rs11712888	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714444	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716558	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717046	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717638	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720745	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914318	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919389	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11924013	0.88[ASN][1000 genomes]
rs11925001	0.91[ASN][1000 genomes]
rs12629954	0.82[ASN][1000 genomes]
rs12631513	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633089	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633770	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635128	0.81[ASN][1000 genomes]
rs12636557	0.91[ASN][1000 genomes]
rs13059470	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060963	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.91[ASN][1000 genomes]
rs13065944	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066768	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068350	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069443	0.90[ASN][1000 genomes]
rs13077703	0.91[ASN][1000 genomes]
rs13078652	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081846	0.91[ASN][1000 genomes]
rs13084113	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084432	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085776	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094911	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096323	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099674	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100262	0.90[ASN][1000 genomes]
rs1460097	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347156	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17347644	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	0.92[ASN][1000 genomes]
rs1963961	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963962	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288272	0.91[ASN][1000 genomes]
rs2290859	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303474	0.91[ASN][1000 genomes]
rs2318090	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094295	0.91[ASN][1000 genomes]
rs3094296	0.91[ASN][1000 genomes]
rs3094297	0.92[ASN][1000 genomes]
rs3109756	0.89[ASN][1000 genomes]
rs34063583	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263427	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.87[ASN][1000 genomes]
rs34376498	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624546	0.91[ASN][1000 genomes]
rs34648996	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34743741	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34883763	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34947019	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34963630	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35315807	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35799195	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35810977	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35850993	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36002990	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36060163	0.82[ASN][1000 genomes]
rs3806653	0.92[ASN][1000 genomes]
rs3806654	0.92[ASN][1000 genomes]
rs3864012	0.86[ASN][1000 genomes]
rs4342086	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55654108	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55821257	0.81[ASN][1000 genomes]
rs55859364	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56291106	0.91[ASN][1000 genomes]
rs58658478	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59596156	0.91[ASN][1000 genomes]
rs61396602	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.91[ASN][1000 genomes]
rs62284198	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284199	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768327	0.83[ASN][1000 genomes]
rs71625262	0.87[ASN][1000 genomes]
rs7628866	0.82[ASN][1000 genomes]
rs7629753	0.91[ASN][1000 genomes]
rs7645391	0.82[ASN][1000 genomes]
rs7651406	0.88[ASN][1000 genomes]
rs7651721	0.91[ASN][1000 genomes]
rs9830943	0.93[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	nsv963500	chr3:101481412-101496033	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13077925	NXPE3	cis	Esophagus Muscularis	GTEx
rs13077925	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101472800-101488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:101474800-101490600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:101475600-101488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:101477200-101497400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:101477400-101497600	Weak transcription	Right Ventricle	heart
7	chr3:101477600-101488400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:101477600-101488400	Weak transcription	Spleen	Spleen
9	chr3:101477600-101497400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:101478000-101489000	Weak transcription	Gastric	stomach
11	chr3:101478000-101497400	Weak transcription	NHEK	skin
12	chr3:101478600-101488400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:101478600-101489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:101478600-101497400	Weak transcription	A549	lung
15	chr3:101478600-101497400	Weak transcription	K562	blood
16	chr3:101478800-101488200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:101478800-101490400	Weak transcription	Ovary	ovary
18	chr3:101479000-101488400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:101479000-101497400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:101479200-101490000	Weak transcription	Fetal Kidney	kidney
21	chr3:101479200-101497400	Weak transcription	NHLF	lung
22	chr3:101480400-101497400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:101482000-101497400	Weak transcription	HUVEC	blood vessel
24	chr3:101483000-101491200	Weak transcription	HSMMtube	muscle
25	chr3:101483000-101497400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:101483200-101497400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:101483800-101497200	Weak transcription	Fetal Stomach	stomach
28	chr3:101484200-101489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:101484200-101497400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:101484200-101497400	Weak transcription	Hela-S3	cervix
31	chr3:101484200-101497400	Weak transcription	NHDF-Ad	bronchial
32	chr3:101484400-101489000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:101484400-101489000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:101484400-101489800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:101484400-101495800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:101484400-101496400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:101484400-101497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:101484400-101497200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:101484400-101497200	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:101484400-101497200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:101484400-101497200	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:101484400-101497400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:101484400-101497400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:101484400-101497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:101484400-101497400	Weak transcription	Brain Substantia Nigra	brain
46	chr3:101484400-101497400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:101484400-101497400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:101484400-101497400	Weak transcription	NH-A	brain
49	chr3:101484400-101497400	Weak transcription	Osteobl	bone
50	chr3:101484400-101497600	Weak transcription	Liver	Liver

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