Variant report

Variant	rs1016428
Chromosome Location	chr9:104401535-104401536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10118878	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10120502	0.80[ASN][1000 genomes]
rs10760797	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10819957	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819966	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10989564	0.85[AFR][1000 genomes]
rs10989566	0.89[AFR][1000 genomes]
rs10989567	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989568	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989573	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989574	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351943	0.85[EUR][1000 genomes]
rs12352862	0.86[EUR][1000 genomes]
rs12685902	0.83[ASN][1000 genomes]
rs1323431	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13290305	0.82[ASN][1000 genomes]
rs1407871	0.86[EUR][1000 genomes]
rs1407872	0.84[EUR][1000 genomes]
rs1407876	0.86[ASN][1000 genomes]
rs1570514	0.93[AFR][1000 genomes]
rs1951781	0.86[EUR][1000 genomes]
rs2067056	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2485522	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2485525	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2485528	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2485533	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2485534	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4742820	0.93[AFR][1000 genomes]
rs4743474	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7035242	0.86[EUR][1000 genomes]
rs7849782	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1016428	GALNT12	cis	cerebellum	SCAN
rs1016428	TMOD1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104399000-104403400	Enhancers	Liver	Liver
2	chr9:104399200-104402600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:104401000-104403200	Enhancers	Fetal Lung	lung
4	chr9:104401200-104402800	Enhancers	Pancreatic Islets	Pancreatic Islet

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