Variant report

Variant	rs9548026
Chromosome Location	chr13:38282470-38282471
allele	G/T
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:32)

rs_ID	r²[population]
rs1041018	0.81[AMR][1000 genomes]
rs11147662	0.81[CEU][hapmap]
rs11843893	0.81[CEU][hapmap]
rs12429617	0.92[AFR][1000 genomes]
rs1413002	1.00[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs28646275	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4941876	0.82[AMR][1000 genomes]
rs56312513	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59082193	0.91[EUR][1000 genomes]
rs7321585	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7321872	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7330679	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9532093	0.95[CEU][hapmap]
rs9532095	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9532101	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9532105	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532106	0.90[AFR][1000 genomes]
rs9547965	0.88[CEU][hapmap]
rs9547991	0.81[CEU][hapmap]
rs9547994	0.95[CEU][hapmap]
rs9547996	0.95[CEU][hapmap]
rs9547997	0.95[CEU][hapmap]
rs9547998	0.95[CEU][hapmap]
rs9547999	0.94[CEU][hapmap]
rs9548000	0.95[CEU][hapmap];0.82[TSI][hapmap]
rs9548003	1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs9548008	0.91[EUR][1000 genomes]
rs9548029	0.85[AFR][1000 genomes]
rs9548030	0.87[AFR][1000 genomes]
rs9548031	0.84[AFR][1000 genomes]
rs9548032	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs978156	1.00[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv976233	chr13:38280432-38284114	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9548026	POSTN	cis	cerebellum	SCAN
rs9548026	LOC646982	cis	parietal	SCAN
rs9548026	SOHLH2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38276800-38289200	Weak transcription	NH-A	brain
2	chr13:38277400-38288600	Weak transcription	Osteobl	bone
3	chr13:38281800-38282600	Enhancers	NHDF-Ad	bronchial
4	chr13:38282200-38282600	Enhancers	Colon Smooth Muscle	Colon
5	chr13:38282200-38283200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:38282200-38284200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr13:38282200-38284600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:38282200-38289200	Weak transcription	Ovary	ovary
9	chr13:38282400-38284200	Weak transcription	NHLF	lung
10	chr13:38282400-38284800	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links