Variant report

Variant	rs866129
Chromosome Location	chr1:97696711-97696712
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10783056	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875056	0.94[EUR][1000 genomes]
rs10875057	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875058	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11165815	0.87[ASN][1000 genomes]
rs12402250	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403951	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333727	0.83[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1413239	0.85[EUR][1000 genomes]
rs1520658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1520663	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1520664	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1760212	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1931072	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2027054	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2039447	0.83[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2039448	0.85[EUR][1000 genomes]
rs3897933	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4415625	0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4511173	0.83[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs493517	0.84[ASN][1000 genomes]
rs495257	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs563033	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs563832	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs576189	0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs61637399	0.85[EUR][1000 genomes]
rs666924	0.86[ASN][1000 genomes]
rs827497	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs864335	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs865242	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs866129	CDC14A	cis	parietal	SCAN
rs866129	GPR88	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97659000-97697000	Weak transcription	Liver	Liver
2	chr1:97660600-97698600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:97663600-97698600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:97666600-97697400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:97678200-97698600	Weak transcription	Left Ventricle	heart
6	chr1:97678400-97697400	Weak transcription	Dnd41	blood
7	chr1:97690400-97698800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:97690800-97698600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:97691400-97698600	Weak transcription	Gastric	stomach
10	chr1:97691400-97701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:97691400-97702600	Weak transcription	Fetal Intestine Small	intestine
12	chr1:97692800-97703400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:97693000-97701800	Weak transcription	Fetal Lung	lung
14	chr1:97693200-97700800	Weak transcription	Pancreas	Pancrea
15	chr1:97694000-97699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:97694400-97698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:97694600-97698600	Weak transcription	Ovary	ovary
18	chr1:97694800-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:97694800-97698600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:97694800-97698600	Weak transcription	Esophagus	oesophagus
21	chr1:97694800-97698800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:97694800-97698800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:97694800-97701000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:97694800-97712800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:97695000-97698600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:97695000-97698600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:97695000-97698600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:97695400-97698800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:97695600-97697800	Strong transcription	Primary B cells from cord blood	blood
30	chr1:97695800-97697400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:97695800-97700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:97696000-97698400	Weak transcription	HSMM	muscle
33	chr1:97696000-97698600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:97696000-97698800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:97696000-97701000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:97696200-97697400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr1:97696200-97698600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:97696400-97698000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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