Variant report

Variant	rs10869801
Chromosome Location	chr9:79335621-79335622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10512061	0.84[JPT][hapmap]
rs10735649	0.85[JPT][hapmap]
rs10869802	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869804	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10869805	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10869806	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145017	0.81[CHB][hapmap];0.88[MEX][hapmap]
rs11145018	0.80[CHB][hapmap]
rs11145021	0.81[CHB][hapmap];0.94[MEX][hapmap]
rs11145023	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12238013	0.81[CHB][hapmap];0.94[MEX][hapmap]
rs12552182	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553799	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683741	0.86[AMR][1000 genomes]
rs1329015	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329016	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329017	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329018	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536820	0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2077181	0.88[MEX][hapmap]
rs2277155	0.81[CHB][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs35141311	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739521	0.81[MEX][hapmap]
rs3739524	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs488165	0.84[JPT][hapmap]
rs519983	0.84[JPT][hapmap]
rs530978	0.84[JPT][hapmap]
rs551262	0.84[JPT][hapmap]
rs571960	0.84[JPT][hapmap]
rs57347426	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57608282	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58286902	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620985	0.84[JPT][hapmap]
rs630423	0.84[JPT][hapmap]
rs684639	0.81[JPT][hapmap]
rs685011	0.84[JPT][hapmap]
rs7042953	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs724017	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9314853	0.86[AMR][1000 genomes]
rs9785303	0.81[CHB][hapmap];0.94[MEX][hapmap]

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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10869801	PRUNE2	cis	cerebellum	SCAN
rs10869801	VPS13A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
2	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
3	chr9:79333000-79340000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:79333200-79338200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:79333200-79346800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79333200-79359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:79333600-79342200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:79333600-79344000	Weak transcription	HSMMtube	muscle
10	chr9:79333800-79341000	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:79333800-79342200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:79333800-79347800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:79334000-79339800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links