Variant report

Variant	rs9525017
Chromosome Location	chr13:96194528-96194529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1000601	0.84[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11843974	0.84[CEU][hapmap]
rs12427460	0.84[CEU][hapmap]
rs1952107	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771917	0.85[CEU][hapmap]
rs4771920	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771921	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773919	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs59483123	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72651928	0.85[EUR][1000 genomes]
rs7995795	0.84[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs8001332	0.80[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs927786	0.88[CEU][hapmap]
rs927787	0.84[CEU][hapmap]
rs927788	0.84[CEU][hapmap]
rs9302075	0.84[CEU][hapmap]
rs9302076	0.84[CEU][hapmap]
rs9516600	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516601	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516602	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524989	0.87[CEU][hapmap]
rs9524991	0.84[CEU][hapmap]
rs9524994	0.80[CEU][hapmap]
rs9525011	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9525016	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9525018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525019	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525025	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9525026	0.80[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9525028	0.84[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9525029	0.86[EUR][1000 genomes]
rs9525030	0.85[EUR][1000 genomes]
rs9525032	0.80[CEU][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9525017	UGCGL2	cis	multi-tissue	Pritchard
rs9525017	FARP1	cis	cerebellum	SCAN
rs9525017	CLDN10	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96188000-96199600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:96188400-96198800	Weak transcription	Hela-S3	cervix
3	chr13:96189600-96198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:96189800-96199000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:96192600-96194600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:96192600-96194600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr13:96192600-96194600	Enhancers	Pancreas	Pancrea
8	chr13:96192600-96195000	Enhancers	Fetal Muscle Leg	muscle
9	chr13:96192800-96194600	Enhancers	Fetal Heart	heart
10	chr13:96193200-96194600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr13:96193200-96194600	Enhancers	Primary hematopoietic stem cells	blood
12	chr13:96193200-96194600	Enhancers	Psoas Muscle	Psoas
13	chr13:96193200-96194600	Enhancers	HUVEC	blood vessel
14	chr13:96193600-96194600	Enhancers	HSMMtube	muscle
15	chr13:96193800-96195400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr13:96193800-96198800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr13:96194000-96194800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:96194200-96194600	Enhancers	Osteobl	bone
19	chr13:96194200-96194800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr13:96194200-96199600	Weak transcription	A549	lung
21	chr13:96194400-96194600	Enhancers	Brain Anterior Caudate	brain
22	chr13:96194400-96195200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links