Variant report

Variant	rs17197320
Chromosome Location	chr9:104401909-104401910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10117054	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10121600	0.87[CHB][hapmap]
rs10123455	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512287	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11791232	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11791256	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11792639	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000109	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13284303	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287159	1.00[ASN][1000 genomes]
rs13287476	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13289614	1.00[ASN][1000 genomes]
rs13292935	1.00[ASN][1000 genomes]
rs13298667	0.89[ASN][1000 genomes]
rs13301163	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572563	0.83[AFR][1000 genomes]
rs17199409	0.89[ASN][1000 genomes]
rs17200616	0.83[AFR][1000 genomes]
rs1832333	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs1853448	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181561	1.00[ASN][1000 genomes]
rs33945236	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35153081	1.00[ASN][1000 genomes]
rs35230964	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35320813	1.00[ASN][1000 genomes]
rs35501099	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35698290	0.97[ASN][1000 genomes]
rs35728981	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35778437	0.97[ASN][1000 genomes]
rs36074111	0.95[ASN][1000 genomes]
rs36091868	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71509736	1.00[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
rs17197320	C9orf30	cis	cerebellum	SCAN
rs17197320	NANS	cis	cerebellum	SCAN

Chromatin state (count:9 , 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
5	chr9:104401600-104402400	Enhancers	Colon Smooth Muscle	Colon
6	chr9:104401600-104402800	Weak transcription	Pancreas	Pancrea
7	chr9:104401800-104402000	Enhancers	Rectal Smooth Muscle	rectum
8	chr9:104401800-104402200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr9:104401800-104402200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links