Variant report

Variant	rs2318090
Chromosome Location	chr3:101474933-101474934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031710	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	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707250	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710805	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711079	0.91[ASN][1000 genomes]
rs11711903	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712309	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712748	0.91[ASN][1000 genomes]
rs11712888	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714278	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714444	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716558	0.94[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	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720745	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914318	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	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633089	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633770	0.80[AMR][1000 genomes];0.85[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	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061565	0.91[ASN][1000 genomes]
rs13065944	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066768	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069443	0.90[ASN][1000 genomes]
rs13077703	0.91[ASN][1000 genomes]
rs13077925	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078652	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081846	0.91[ASN][1000 genomes]
rs13084113	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084432	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085776	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094753	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094911	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096323	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099674	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100262	0.90[ASN][1000 genomes]
rs1460097	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347156	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17347644	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17411983	0.92[ASN][1000 genomes]
rs1963961	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	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303474	0.91[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	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161138	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263427	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34301719	0.87[ASN][1000 genomes]
rs34376498	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624546	0.91[ASN][1000 genomes]
rs34648996	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34743741	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34883763	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34947019	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34963630	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117343	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35315807	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35799195	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35810977	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35850993	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36002990	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	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55654108	0.81[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	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59596156	0.91[ASN][1000 genomes]
rs61396602	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62282218	0.91[ASN][1000 genomes]
rs62284198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62284199	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768327	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];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: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
rs2318090	NXPE3	cis	Esophagus Muscularis	GTEx
rs2318090	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101451800-101476600	Weak transcription	Psoas Muscle	Psoas
3	chr3:101453400-101478400	Weak transcription	Small Intestine	intestine
4	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:101454600-101476400	Weak transcription	NHEK	skin
6	chr3:101454600-101476600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:101454800-101476600	Weak transcription	A549	lung
8	chr3:101455200-101476600	Weak transcription	Pancreas	Pancrea
9	chr3:101455400-101476200	Weak transcription	NHLF	lung
10	chr3:101455400-101476600	Weak transcription	Right Ventricle	heart
11	chr3:101455400-101476600	Weak transcription	K562	blood
12	chr3:101455400-101477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:101455600-101476800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:101455800-101475400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:101464000-101476400	Weak transcription	Fetal Brain Male	brain
16	chr3:101464200-101486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:101465400-101478400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:101470400-101476600	Weak transcription	Fetal Kidney	kidney
19	chr3:101470600-101476600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:101471400-101476600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:101471800-101479400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:101472800-101478800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:101472800-101488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:101473000-101477800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:101473000-101478600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:101473000-101478600	Strong transcription	Fetal Lung	lung
27	chr3:101473000-101478600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:101473000-101478800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:101473000-101479000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:101473000-101479000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:101473000-101479000	Strong transcription	HSMM	muscle
32	chr3:101473000-101479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:101473000-101480800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:101473000-101484400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:101473000-101485400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:101473000-101485400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:101473000-101486000	Strong transcription	Dnd41	blood
38	chr3:101473200-101478800	Strong transcription	Fetal Stomach	stomach
39	chr3:101473200-101479200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:101473400-101475000	Strong transcription	Hela-S3	cervix
41	chr3:101473400-101476200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:101473400-101477200	Strong transcription	HUVEC	blood vessel
43	chr3:101473400-101478400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:101473400-101478600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:101473400-101479000	Genic enhancers	Brain Hippocampus Middle	brain
46	chr3:101473400-101479200	Strong transcription	Left Ventricle	heart
47	chr3:101473400-101484600	Strong transcription	Fetal Thymus	thymus
48	chr3:101473600-101475800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:101473600-101477600	Strong transcription	HSMMtube	muscle
50	chr3:101473600-101477800	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links