Variant report

Variant	rs7029133
Chromosome Location	chr9:85686645-85686646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1008171	0.84[CEU][hapmap]
rs1010480	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10115768	0.85[AMR][1000 genomes]
rs10116216	0.85[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10116254	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs10121204	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs10121395	0.96[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes]
rs10126033	0.87[AMR][1000 genomes]
rs10735559	0.85[CEU][hapmap]
rs10746694	0.86[AMR][1000 genomes]
rs10780561	0.87[CEU][hapmap]
rs10780562	0.95[CEU][hapmap]
rs10780563	0.96[CEU][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes]
rs10780565	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs10780567	0.96[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs10867924	0.86[AMR][1000 genomes]
rs10867925	0.91[AMR][1000 genomes]
rs10867926	0.89[AMR][1000 genomes]
rs10867927	0.86[AMR][1000 genomes]
rs10867928	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs10867929	0.96[CEU][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13302349	0.86[AMR][1000 genomes]
rs1393562	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1393563	0.85[CEU][hapmap]
rs1393564	0.89[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs1393565	0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs1502682	0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs1502683	0.85[CEU][hapmap]
rs1502684	0.85[CEU][hapmap]
rs1502685	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes]
rs1546315	0.96[CEU][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs1546316	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1546317	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1580881	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1976455	0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes]
rs1995423	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs2279814	0.96[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs2378646	0.84[CHB][hapmap]
rs29001503	0.87[AMR][1000 genomes]
rs4146960	0.96[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes]
rs4146961	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs4301515	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs4311721	0.84[CHB][hapmap]
rs4348583	0.92[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes]
rs4355855	0.85[CEU][hapmap]
rs4385545	0.96[CEU][hapmap];0.87[GIH][hapmap]
rs4391505	0.85[CEU][hapmap]
rs4460464	0.85[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4623517	0.96[CEU][hapmap];0.87[GIH][hapmap]
rs4628323	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4877244	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes]
rs4877725	0.85[CEU][hapmap]
rs4877726	0.82[CEU][hapmap]
rs6559694	0.96[CEU][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes]
rs6559695	0.92[CEU][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs7019227	0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7024864	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs7043325	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045914	0.81[AMR][1000 genomes]
rs7847666	0.96[CEU][hapmap];0.82[AMR][1000 genomes]
rs7854101	0.96[CEU][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs7866666	0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7867614	0.85[AMR][1000 genomes]
rs871512	0.82[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs952450	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs998119	0.87[AMR][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	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1043722	chr9:85663674-85747562	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv831642	chr9:85679425-85817338	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831643	chr9:85679431-85798990	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7029133	AGTPBP1	cis	parietal	SCAN
rs7029133	WNT10B	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85679200-85687800	Weak transcription	Fetal Intestine Small	intestine
2	chr9:85682400-85706200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:85683800-85687200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:85685000-85696600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:85686400-85687200	Strong transcription	Pancreas	Pancrea
6	chr9:85686600-85686800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
7	chr9:85686600-85687000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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