Variant report

Variant	rs10117340
Chromosome Location	chr9:98794812-98794813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98793079..98797604-chr9:98797988..98801744,7	MCF-7	breast:
2	chr9:98790248..98792722-chr9:98793401..98795775,2	MCF-7	breast:
3	chr9:98790389..98794152-chr9:98794649..98798124,5	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10115110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512242	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10512245	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10739705	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10760189	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs10760261	0.90[CEU][hapmap]
rs10760269	0.90[CEU][hapmap]
rs10760679	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10818574	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs10818899	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10819650	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10819663	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10819668	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10819720	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10985156	0.80[AMR][1000 genomes]
rs10985499	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap]
rs10987963	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10988755	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10988817	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10989035	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1195130	0.94[AMR][1000 genomes]
rs11998982	0.81[AMR][1000 genomes]
rs12340954	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12345187	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12347675	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12348051	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12349742	0.90[CEU][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1327996	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1327997	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13294931	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap]
rs13298093	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13299166	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs1556026	0.91[EUR][1000 genomes]
rs2026031	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2296858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405372	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2943532	0.95[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4291387	1.00[ASW][hapmap]
rs589362	0.95[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs596413	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs603947	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs609296	0.85[AMR][1000 genomes]
rs617187	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs623438	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs624075	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs625105	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62559026	0.85[AMR][1000 genomes]
rs62559767	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs640297	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs649819	0.95[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs657451	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs666093	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs667705	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs671058	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs682682	0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs684455	0.95[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs686048	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689619	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689696	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs689697	0.90[CEU][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689710	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689738	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689761	0.95[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689804	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs689860	0.81[AMR][1000 genomes]
rs689911	0.82[AMR][1000 genomes]
rs689986	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs690056	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690063	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs690495	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690528	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690633	0.90[CEU][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes]
rs694230	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847393	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847983	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816682	0.82[AMR][1000 genomes]
rs816683	0.81[AMR][1000 genomes]
rs816684	0.81[AMR][1000 genomes]
rs966217	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10117340	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10117340	C9orf102	cis	lymphoblastoid	seeQTL
rs10117340	IPPK	cis	cerebellum	SCAN
rs10117340	C9orf130	cis	cerebellum	SCAN
rs10117340	ERCC6L2	cis	Artery Tibial	GTEx
rs10117340	C9orf130	cis	lymphoblastoid	seeQTL
rs10117340	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs10117340	C9orf102	cis	multi-tissue	Pritchard
rs10117340	C9orf130	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790200-98795800	Weak transcription	Esophagus	oesophagus
2	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
3	chr9:98791200-98796800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:98792000-98795200	Enhancers	Ovary	ovary
5	chr9:98793600-98800800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:98793600-98804600	Weak transcription	Fetal Heart	heart
7	chr9:98794200-98796800	Weak transcription	Fetal Intestine Small	intestine
8	chr9:98794200-98797000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:98794400-98795000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:98794400-98796200	Weak transcription	Brain Anterior Caudate	brain
11	chr9:98794400-98796400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:98794400-98797800	Weak transcription	Fetal Lung	lung
13	chr9:98794400-98801000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:98794600-98796600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:98794600-98799400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links