Variant report

Variant	rs56291106
Chromosome Location	chr3:101377474-101377475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1031710	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710533	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712748	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717046	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720745	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923273	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11924013	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635128	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	0.86[ASN][1000 genomes]
rs13066768	0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17411983	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303474	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094296	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.91[ASN][1000 genomes]
rs34624546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806653	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55654108	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59596156	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62284162	0.81[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56291106	NXPE3	cis	Esophagus Muscularis	GTEx
rs56291106	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101362800-101391600	Weak transcription	Stomach Mucosa	stomach
2	chr3:101363000-101381800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:101363400-101382800	Weak transcription	Fetal Heart	heart
6	chr3:101363400-101391400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:101364800-101391000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:101364800-101391000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:101364800-101392000	Strong transcription	Primary T cells from cord blood	blood
10	chr3:101365000-101378000	Weak transcription	Fetal Brain Male	brain
11	chr3:101365200-101387800	Strong transcription	Liver	Liver
12	chr3:101365400-101385400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr3:101366000-101384800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:101366400-101390400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:101366400-101392200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:101366600-101380400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:101366600-101390800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:101366600-101390800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:101366600-101391000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:101366600-101391000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr3:101366600-101391000	Strong transcription	Fetal Thymus	thymus
22	chr3:101366600-101391800	Strong transcription	Primary B cells from cord blood	blood
23	chr3:101366800-101380000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:101366800-101390400	Strong transcription	Fetal Lung	lung
25	chr3:101366800-101391000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:101366800-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:101367000-101384600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:101367000-101390800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:101367000-101390800	Strong transcription	Dnd41	blood
30	chr3:101367000-101391000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:101367000-101391000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:101367000-101391000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:101367000-101391000	Strong transcription	Placenta	Placenta
34	chr3:101367000-101391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:101367200-101385400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:101367200-101391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:101367200-101391800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:101367400-101391000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:101367400-101391000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:101367600-101390400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:101367800-101380200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:101367800-101380400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:101368000-101378000	Weak transcription	NHLF	lung
44	chr3:101368000-101381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:101368000-101383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:101368000-101390600	Strong transcription	Adipose Nuclei	Adipose
47	chr3:101368000-101391000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:101368000-101391600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:101368200-101380200	Strong transcription	Osteobl	bone
50	chr3:101368200-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links