Variant report

Variant	rs9291685
Chromosome Location	chr5:59556271-59556272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10064516	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10074696	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10077172	0.89[YRI][hapmap]
rs10079009	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523473	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1862614	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4235479	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410606	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4604150	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4700370	0.94[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5024245	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59518781	0.97[ASN][1000 genomes]
rs6449459	0.82[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6862158	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6864705	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882437	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7444733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs7710822	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7714765	0.92[GIH][hapmap];0.87[TSI][hapmap]
rs7728100	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs7734400	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291686	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv4847	chr5:59523591-59569307	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9291685	SLC2A4	trans	cerebellum	SCAN
rs9291685	ELOVL7	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59554200-59557600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:59554200-59562400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:59554400-59561600	Weak transcription	HepG2	liver
4	chr5:59554800-59559600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:59555000-59556800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr5:59555000-59557200	Enhancers	Hela-S3	cervix
7	chr5:59555000-59558800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr5:59555200-59556600	Enhancers	Primary hematopoietic stem cells	blood
9	chr5:59555200-59557600	Enhancers	Primary B cells from cord blood	blood
10	chr5:59555400-59556400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:59555400-59557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:59555800-59557600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:59556000-59556600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:59556000-59556800	Enhancers	HUVEC	blood vessel
15	chr5:59556200-59557200	Enhancers	Muscle Satellite Cultured Cells	--

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