Variant report

Variant	rs3731754
Chromosome Location	chr2:179368916-179368917
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179368274..179373931-chr2:179383180..179392063,9	K562	blood:
2	chr2:179342810..179345540-chr2:179367269..179371367,3	MCF-7	breast:
3	chr2:179368753..179371424-chr2:179372285..179374100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000079150	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1001238	0.85[CHB][hapmap]
rs10207436	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10930831	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12052983	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13411588	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1559908	1.00[JPT][hapmap]
rs1560221	0.85[CHB][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16866400	0.85[CHB][hapmap]
rs16866420	0.85[CHB][hapmap]
rs1978580	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2016615	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042996	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2059691	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2114582	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2163009	0.85[CHB][hapmap]
rs2249737	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs2288322	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2366751	0.85[CHB][hapmap]
rs2742351	0.81[CHB][hapmap]
rs2886712	0.85[ASN][1000 genomes]
rs33998881	0.80[ASN][1000 genomes]
rs3731750	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3752689	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769864	0.80[CHB][hapmap]
rs3769866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813250	0.80[CHB][hapmap]
rs3829746	0.85[CHB][hapmap]
rs4894017	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4894018	0.94[CEU][hapmap]
rs4894020	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4894029	0.85[CHB][hapmap]
rs4894030	0.81[CHB][hapmap]
rs60488846	0.80[ASN][1000 genomes]
rs6704545	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6710856	0.89[ASN][1000 genomes]
rs6723399	0.86[ASN][1000 genomes]
rs6726043	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6735077	0.83[ASN][1000 genomes]
rs6739142	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6753709	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6758838	0.88[ASN][1000 genomes]
rs7575643	1.00[JPT][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7588593	0.80[ASN][1000 genomes]
rs7589679	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7598228	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7600176	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7602597	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9288019	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs957875	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs967507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808377	0.85[CHB][hapmap]
rs9967820	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3731754	PLEKHA3	cis	Lymphoblastoid	GTEx
rs3731754	ENSG00000116095	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:179347400-179369400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:179347600-179371000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:179350400-179371600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:179350400-179371600	Strong transcription	Dnd41	blood
6	chr2:179350400-179372400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:179350400-179372400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:179350400-179384400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:179350600-179371200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr2:179350600-179372200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:179350800-179370600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:179350800-179371600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:179350800-179372000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:179350800-179372000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:179352800-179372200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:179353400-179369000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:179353600-179371600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179354000-179371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:179354400-179371400	Strong transcription	Placenta	Placenta
20	chr2:179354400-179371600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:179354400-179372000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:179354600-179370000	Strong transcription	Liver	Liver
23	chr2:179354600-179373000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:179354600-179373000	Strong transcription	HSMM	muscle
25	chr2:179355200-179369000	Strong transcription	Fetal Intestine Large	intestine
26	chr2:179358200-179369600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:179358200-179369800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr2:179358200-179372800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:179358600-179370000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:179358600-179370000	Strong transcription	Adipose Nuclei	Adipose
31	chr2:179358600-179370600	Strong transcription	Fetal Thymus	thymus
32	chr2:179359400-179371000	Weak transcription	Colonic Mucosa	Colon
33	chr2:179359400-179382800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:179359600-179371400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:179359600-179387600	Weak transcription	Right Ventricle	heart
36	chr2:179359600-179387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:179360600-179382400	Weak transcription	Gastric	stomach
38	chr2:179360600-179383200	Weak transcription	Pancreas	Pancrea
39	chr2:179360800-179369600	Weak transcription	Esophagus	oesophagus
40	chr2:179360800-179376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:179360800-179383000	Weak transcription	Aorta	Aorta
42	chr2:179360800-179387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:179361000-179387800	Weak transcription	Spleen	Spleen
44	chr2:179361400-179371600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:179361400-179387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:179362000-179370200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:179362200-179369600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:179362200-179371400	Weak transcription	Fetal Intestine Small	intestine
49	chr2:179362200-179371400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr2:179362200-179374000	Weak transcription	Fetal Stomach	stomach

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