Variant report

Variant	rs2240119
Chromosome Location	chr17:46111172-46111173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1133221	0.94[GIH][hapmap]
rs12051	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs12600980	0.86[EUR][1000 genomes]
rs12601350	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12602131	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12602670	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946143	0.89[EUR][1000 genomes]
rs1452663	0.91[CEU][hapmap]
rs1468270	0.86[JPT][hapmap]
rs1473117	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16949270	0.94[GIH][hapmap]
rs16951519	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs16953941	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17616799	0.94[GIH][hapmap]
rs1860862	0.81[JPT][hapmap]
rs1979897	0.91[CEU][hapmap]
rs2023885	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2041572	0.81[JPT][hapmap]
rs208005	0.83[CEU][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs208008	0.94[GIH][hapmap];0.90[TSI][hapmap]
rs208009	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs208015	0.87[GIH][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs2229369	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs2240120	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2240121	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2285860	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs2325783	0.95[EUR][1000 genomes]
rs2325804	0.91[CEU][hapmap]
rs2525105	1.00[GIH][hapmap]
rs3764400	1.00[MKK][hapmap]
rs3785737	0.83[EUR][1000 genomes]
rs4793779	0.83[CHB][hapmap]
rs4995899	0.93[EUR][1000 genomes]
rs55920502	0.93[EUR][1000 genomes]
rs55982711	0.85[EUR][1000 genomes]
rs58554000	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224461	0.82[CEU][hapmap]
rs72823519	0.85[EUR][1000 genomes]
rs72823528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823532	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs758999	0.81[JPT][hapmap]
rs8066049	0.82[EUR][1000 genomes]
rs8071199	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs8071879	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs978263	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9890691	0.83[EUR][1000 genomes]
rs9898218	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs9944405	0.83[GIH][hapmap]

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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2240119	CBX1	cis	cerebellum	SCAN
rs2240119	KRT37	cis	cerebellum	SCAN
rs2240119	SNX11	cis	multi-tissue	Pritchard
rs2240119	HOXB2	cis	multi-tissue	Pritchard
rs2240119	CDK5RAP3	cis	cerebellum	SCAN
rs2240119	TUBG1	cis	parietal	SCAN
rs2240119	CDK5RAP3	cis	parietal	SCAN
rs2240119	DHX58	cis	parietal	SCAN
rs2240119	HSPB9	cis	parietal	SCAN
rs2240119	HOXB7	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46104200-46113800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:46104400-46114000	Weak transcription	Liver	Liver
3	chr17:46104400-46114000	Weak transcription	Right Ventricle	heart
4	chr17:46104400-46114200	Weak transcription	Brain Substantia Nigra	brain
5	chr17:46104600-46113800	Weak transcription	HSMM	muscle
6	chr17:46104600-46114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:46104600-46114000	Weak transcription	Brain Hippocampus Middle	brain
8	chr17:46104800-46113800	Weak transcription	NHDF-Ad	bronchial
9	chr17:46104800-46114000	Weak transcription	HSMMtube	muscle
10	chr17:46105000-46113800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:46105400-46114000	Weak transcription	K562	blood
12	chr17:46105600-46114000	Weak transcription	Pancreas	Pancrea
13	chr17:46108200-46113200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:46108400-46111600	Strong transcription	Fetal Muscle Leg	muscle
15	chr17:46108400-46113800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr17:46108400-46114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:46108400-46114000	Weak transcription	Adipose Nuclei	Adipose
18	chr17:46108400-46114000	Weak transcription	NH-A	brain
19	chr17:46108400-46114200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:46108400-46114200	Weak transcription	Brain Anterior Caudate	brain
21	chr17:46108400-46114200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:46108400-46114200	Weak transcription	Esophagus	oesophagus
23	chr17:46108600-46113800	Weak transcription	Colon Smooth Muscle	Colon
24	chr17:46109000-46111200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:46109000-46111200	Strong transcription	Fetal Stomach	stomach
26	chr17:46109000-46111400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:46109000-46111400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr17:46109000-46111800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr17:46109000-46112600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:46109200-46111200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr17:46109200-46111400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:46109200-46112600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:46109400-46111400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:46109400-46111400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr17:46109400-46111400	Strong transcription	NHLF	lung
36	chr17:46109600-46111600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:46109600-46112600	Strong transcription	Osteobl	bone
38	chr17:46110400-46114000	Weak transcription	Ovary	ovary
39	chr17:46110400-46114000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr17:46110600-46111200	Strong transcription	Aorta	Aorta
41	chr17:46110600-46111400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:46110600-46111400	Strong transcription	Spleen	Spleen
43	chr17:46111000-46111200	Active TSS	Lung	lung
44	chr17:46111000-46111400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:46111000-46111400	Strong transcription	Placenta	Placenta

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