Variant report

Variant	rs10694
Chromosome Location	chr2:37872139-37872140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37866118..37867665-chr2:37869743..37872565,2	MCF-7	breast:
2	chr2:37865948..37868247-chr2:37870789..37872523,2	K562	blood:
3	chr2:37871133..37873297-chr2:37883736..37885444,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1013291	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1013292	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11124595	0.80[ASN][1000 genomes]
rs11883958	0.83[ASN][1000 genomes]
rs12622958	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs13387842	0.95[ASN][1000 genomes]
rs13392288	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13406302	0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs13417833	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13417957	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468663	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468664	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17021174	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2041508	0.94[ASN][1000 genomes]
rs2072419	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2079998	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2098198	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109821	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109822	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2159726	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2191841	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373290	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373292	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3731852	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3731854	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4372883	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4594425	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670210	0.87[CHB][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs4670211	0.82[ASN][1000 genomes]
rs4670748	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs56809883	0.82[ASN][1000 genomes]
rs6544095	0.87[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs6711909	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6722589	0.83[ASN][1000 genomes]
rs6740127	0.88[ASN][1000 genomes]
rs6752119	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6752220	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs6752762	0.94[ASN][1000 genomes]
rs6759224	0.81[CHD][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs7607934	0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs7735	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9742	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10694	CDC42EP3	cis	lymphoblastoid	seeQTL
rs10694	CDC42EP3	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37873200	Weak transcription	Liver	Liver
2	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
3	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
4	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:37863400-37875000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:37863600-37873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:37865600-37873000	Weak transcription	Ovary	ovary
10	chr2:37866600-37875200	Genic enhancers	HSMM	muscle
11	chr2:37866800-37875000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr2:37867200-37875000	Genic enhancers	NHDF-Ad	bronchial
15	chr2:37867400-37872800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:37867400-37874800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:37868000-37872800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:37868000-37873600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:37868000-37875200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:37868000-37876200	Genic enhancers	Osteobl	bone
21	chr2:37868200-37876200	Genic enhancers	NH-A	brain
22	chr2:37868600-37875400	Weak transcription	Fetal Intestine Large	intestine
23	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:37868800-37872600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:37868800-37873400	Strong transcription	Fetal Brain Female	brain
26	chr2:37868800-37874600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:37869200-37873600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:37869400-37872400	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:37869400-37873800	Genic enhancers	GM12878-XiMat	blood
30	chr2:37869400-37876200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:37869600-37872800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:37869600-37873000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:37869600-37873000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:37869800-37875600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:37870000-37873600	Genic enhancers	A549	lung
36	chr2:37870000-37874800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:37870000-37875400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:37870200-37872400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:37870200-37872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:37870200-37872800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:37870200-37873400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:37870200-37874000	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr2:37870200-37874000	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:37870200-37874000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:37870200-37874400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:37870200-37875200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:37870200-37875400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:37870400-37872200	Strong transcription	Fetal Kidney	kidney
49	chr2:37870400-37872600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:37870600-37872600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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