Variant report

Variant	rs9859834
Chromosome Location	chr3:142106351-142106352
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10935460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935462	0.89[ASN][1000 genomes]
rs11916455	0.91[CHB][hapmap]
rs12632726	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12695757	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060437	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061409	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065140	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067197	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070239	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs13080394	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13085261	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs13087972	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13099184	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs1485393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4256152	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs4582075	0.91[CHB][hapmap]
rs62276415	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6786320	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9814159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9836038	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv520523	chr3:141818850-142110818	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	21 gene(s)	inside rSNPs	diseases
6	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
7	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv877557	chr3:142090402-142150204	Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9859834	TRPC1	cis	parietal	SCAN
rs9859834	XRN1	cis	cerebellum	SCAN
rs9859834	PLS1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142046400-142112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:142057400-142111400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:142059400-142111400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:142060800-142111200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:142063600-142111200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:142064600-142111400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:142066800-142115000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:142072400-142114600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:142074000-142113800	Weak transcription	HMEC	breast
10	chr3:142076000-142136400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:142076800-142106400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:142076800-142106600	Weak transcription	Spleen	Spleen
13	chr3:142076800-142120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:142076800-142138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:142080000-142114000	Weak transcription	NHLF	lung
16	chr3:142083200-142106600	Weak transcription	Gastric	stomach
17	chr3:142083200-142113800	Weak transcription	Small Intestine	intestine
18	chr3:142083200-142114200	Weak transcription	A549	lung
19	chr3:142083400-142114800	Weak transcription	HepG2	liver
20	chr3:142083600-142158600	Weak transcription	NHEK	skin
21	chr3:142086200-142111400	Strong transcription	Fetal Thymus	thymus
22	chr3:142091600-142108800	Weak transcription	Right Ventricle	heart
23	chr3:142092800-142111200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:142094000-142114000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:142094400-142111400	Strong transcription	Liver	Liver
26	chr3:142096600-142113800	Weak transcription	HUVEC	blood vessel
27	chr3:142097000-142112600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:142097200-142108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:142098000-142110600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:142098000-142111400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:142098200-142110400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:142098600-142111400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:142099600-142106600	Weak transcription	Aorta	Aorta
34	chr3:142099800-142112600	Weak transcription	Pancreas	Pancrea
35	chr3:142100600-142111200	Strong transcription	Osteobl	bone
36	chr3:142100800-142107400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:142100800-142108200	Weak transcription	Psoas Muscle	Psoas
38	chr3:142101400-142106600	Strong transcription	HSMM	muscle
39	chr3:142101600-142106400	Weak transcription	Thymus	Thymus
40	chr3:142101600-142106600	Weak transcription	Lung	lung
41	chr3:142101600-142108400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:142102600-142106400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:142102600-142107600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:142103000-142106400	Weak transcription	Ovary	ovary
45	chr3:142103800-142106800	ZNF genes & repeats	Primary T cells from cord blood	blood
46	chr3:142104000-142107000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:142104200-142107000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:142104400-142108600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:142104400-142108600	Weak transcription	Fetal Heart	heart
50	chr3:142104400-142111000	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links