Variant report

Variant	rs2485522
Chromosome Location	chr9:104454025-104454026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10118878	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1016428	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760797	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10760802	0.82[EUR][1000 genomes]
rs10760806	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10819957	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819966	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819978	0.84[EUR][1000 genomes]
rs10989567	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10989568	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10989573	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10989574	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1323431	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2050640	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2067056	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs2184959	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2485525	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485528	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2485533	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485534	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3983721	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4278209	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479063	0.82[EUR][1000 genomes]
rs7849782	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7872456	0.81[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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1046590	chr9:104450624-104848588	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2485522	GALNT12	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104454000-104454600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:104454000-104454800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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