Variant report

Variant	rs9548003
Chromosome Location	chr13:38233206-38233207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1006416	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1028728	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11147662	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11618138	0.81[ASN][1000 genomes]
rs11619443	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11843893	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17197908	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17258466	0.84[ASN][1000 genomes]
rs1924298	0.84[ASN][1000 genomes]
rs2209230	0.84[ASN][1000 genomes]
rs28373781	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28646275	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3934220	0.84[ASN][1000 genomes]
rs4432141	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs56312513	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs56361602	0.89[ASN][1000 genomes]
rs59082193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61957483	0.84[ASN][1000 genomes]
rs73184517	0.84[ASN][1000 genomes]
rs7321585	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs7321872	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7330679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7333205	0.84[ASN][1000 genomes]
rs9532090	0.84[ASN][1000 genomes]
rs9532093	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9532095	0.95[CEU][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes]
rs9532101	0.94[EUR][1000 genomes]
rs9532105	0.91[EUR][1000 genomes]
rs9547958	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9547964	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9547965	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9547968	0.84[ASN][1000 genomes]
rs9547974	0.84[ASN][1000 genomes]
rs9547976	0.84[ASN][1000 genomes]
rs9547977	0.84[ASN][1000 genomes]
rs9547985	0.84[ASN][1000 genomes]
rs9547986	0.84[ASN][1000 genomes]
rs9547991	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9547992	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9547994	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9547996	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9547997	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9547998	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9547999	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548000	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548026	1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs9548032	0.89[EUR][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548003	LOC646982	cis	parietal	SCAN
rs9548003	POSTN	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:38221600-38239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:38221800-38239400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:38225600-38246600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr13:38228000-38238200	Weak transcription	Left Ventricle	heart
6	chr13:38228800-38233600	Enhancers	NHDF-Ad	bronchial
7	chr13:38231000-38241200	Weak transcription	Aorta	Aorta
8	chr13:38231400-38233400	Enhancers	HUVEC	blood vessel
9	chr13:38231800-38255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:38232600-38239600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:38233200-38233400	Weak transcription	Osteobl	bone
12	chr13:38233200-38233600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:38233200-38234000	Strong transcription	Ovary	ovary
14	chr13:38233200-38239800	Weak transcription	NHLF	lung

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