Variant report

Variant	rs7020465
Chromosome Location	chr9:71041878-71041879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10116868	0.86[JPT][hapmap]
rs10511958	0.86[JPT][hapmap]
rs10735596	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780922	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10780935	0.84[CEU][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs10780962	0.86[JPT][hapmap]
rs10780963	0.91[JPT][hapmap]
rs10780967	0.82[JPT][hapmap]
rs10868795	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868796	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10868803	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868804	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868851	0.86[JPT][hapmap]
rs10868852	0.86[JPT][hapmap]
rs10868877	0.86[JPT][hapmap]
rs10868879	0.89[JPT][hapmap]
rs11142075	0.81[JPT][hapmap]
rs11142179	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11142199	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11142305	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11142334	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11142335	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11142549	0.86[JPT][hapmap]
rs11142650	0.83[CHD][hapmap]
rs12000789	0.86[JPT][hapmap]
rs12353500	0.91[JPT][hapmap]
rs1353009	0.86[JPT][hapmap]
rs1492822	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1492823	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1492824	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1602751	0.86[EUR][1000 genomes]
rs17056009	0.91[JPT][hapmap]
rs1887889	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976232	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026033	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026034	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149565	0.85[EUR][1000 genomes]
rs4237245	0.81[JPT][hapmap]
rs4744594	0.91[JPT][hapmap]
rs4745015	0.86[EUR][1000 genomes]
rs4745041	0.82[JPT][hapmap]
rs6560144	0.86[JPT][hapmap]
rs7025140	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7029177	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039149	0.82[JPT][hapmap]
rs7039686	0.86[JPT][hapmap]
rs7042123	0.86[JPT][hapmap]

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	nsv427847	chr9:70318730-71153527	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7020465	PGM5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:70997800-71052600	Weak transcription	HSMMtube	muscle
2	chr9:71035800-71042000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:71038600-71046600	Enhancers	Rectal Smooth Muscle	rectum
4	chr9:71040600-71049000	Enhancers	Colon Smooth Muscle	Colon
5	chr9:71040800-71043600	Enhancers	Fetal Lung	lung
6	chr9:71041400-71042200	Genic enhancers	Stomach Smooth Muscle	stomach
7	chr9:71041400-71043800	Enhancers	Fetal Heart	heart
8	chr9:71041600-71042400	Enhancers	Fetal Muscle Leg	muscle
9	chr9:71041600-71042400	Genic enhancers	Left Ventricle	heart
10	chr9:71041600-71042600	Enhancers	Fetal Muscle Trunk	muscle
11	chr9:71041600-71042600	Enhancers	Right Atrium	heart
12	chr9:71041600-71042600	Enhancers	Right Ventricle	heart
13	chr9:71041600-71042800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:71041600-71043400	Enhancers	Aorta	Aorta
15	chr9:71041800-71042000	Enhancers	Spleen	Spleen
16	chr9:71041800-71042200	Genic enhancers	Fetal Stomach	stomach
17	chr9:71041800-71042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:71041800-71042400	Enhancers	NHLF	lung
19	chr9:71041800-71042600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr9:71041800-71043000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr9:71041800-71043400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:71041800-71043600	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links