Variant report

Variant	rs11139338
Chromosome Location	chr9:72174528-72174529
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10123008	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs10746682	0.84[CHB][hapmap]
rs10780527	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10780528	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10780539	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10867825	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10867828	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10867830	0.92[CHB][hapmap]
rs11139361	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330334	0.86[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1411440	0.92[JPT][hapmap]
rs1556211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1854702	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1854703	0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1967880	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1970017	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2026150	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2309515	0.85[JPT][hapmap]
rs3927538	0.80[ASN][1000 genomes]
rs4744913	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4744914	0.99[ASN][1000 genomes]
rs4744917	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744918	0.93[ASN][1000 genomes]
rs4744919	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559643	0.93[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7030393	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7031694	0.86[ASW][hapmap];0.86[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7033141	0.92[ASW][hapmap];0.85[LWK][hapmap];0.94[YRI][hapmap]
rs72719029	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7350265	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850006	0.91[ASN][1000 genomes]
rs7853783	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7864173	0.89[ASN][1000 genomes]
rs7871895	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs986352	0.86[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs987653	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv893437	chr9:72118962-72223176	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1049390	chr9:72168645-72185751	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11139338	GDA	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72163200-72185600	Weak transcription	Aorta	Aorta
2	chr9:72170200-72184200	Weak transcription	Ovary	ovary
3	chr9:72170400-72176000	Weak transcription	Fetal Kidney	kidney
4	chr9:72170600-72175200	Weak transcription	Liver	Liver
5	chr9:72171400-72180000	Weak transcription	Right Atrium	heart
6	chr9:72173800-72188400	Weak transcription	Fetal Lung	lung

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