Variant report

Variant	rs11138566
Chromosome Location	chr9:72036369-72036370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10116389	0.86[JPT][hapmap]
rs10217407	0.85[JPT][hapmap]
rs10283713	0.85[JPT][hapmap]
rs10283788	0.85[JPT][hapmap]
rs1029064	0.82[CHB][hapmap]
rs1029065	0.85[JPT][hapmap]
rs10746594	0.85[JPT][hapmap]
rs10780344	0.81[JPT][hapmap]
rs10780360	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780361	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10867423	0.92[JPT][hapmap]
rs10867477	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10867481	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10867647	0.81[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs10867671	0.85[JPT][hapmap]
rs10867672	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs1113067	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs11138491	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11138581	0.85[ASN][1000 genomes]
rs11138927	0.81[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs11138980	0.85[JPT][hapmap]
rs11138986	0.82[JPT][hapmap]
rs11139043	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs11139050	0.85[JPT][hapmap]
rs11139160	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11139181	0.85[JPT][hapmap]
rs11788742	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs12235168	0.81[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs12238067	0.85[JPT][hapmap]
rs12344522	0.82[JPT][hapmap]
rs12348063	0.82[JPT][hapmap]
rs1331972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331979	0.82[JPT][hapmap]
rs1334312	0.86[JPT][hapmap]
rs1929896	0.86[JPT][hapmap]
rs2244720	0.86[JPT][hapmap]
rs2297421	0.84[JPT][hapmap]
rs2309431	0.86[JPT][hapmap]
rs2777866	0.86[JPT][hapmap]
rs2777878	0.86[JPT][hapmap]
rs2781521	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs2781522	0.86[JPT][hapmap]
rs2781527	0.83[ASN][1000 genomes]
rs28564328	0.80[ASN][1000 genomes]
rs35625426	0.83[ASN][1000 genomes]
rs3793613	0.80[ASN][1000 genomes]
rs3858105	0.81[JPT][hapmap]
rs3897966	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs3934600	0.86[JPT][hapmap]
rs4237234	0.86[JPT][hapmap]
rs4483220	0.86[JPT][hapmap]
rs4484762	0.86[JPT][hapmap]
rs4744570	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4744886	0.81[JPT][hapmap]
rs4744894	0.86[JPT][hapmap]
rs4744895	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744910	0.85[JPT][hapmap]
rs4744911	0.85[JPT][hapmap]
rs62570234	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62570235	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62570236	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62570237	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62570239	0.82[ASN][1000 genomes]
rs6559488	0.81[JPT][hapmap]
rs6559489	0.81[JPT][hapmap]
rs6559498	0.92[JPT][hapmap]
rs6559513	0.85[JPT][hapmap]
rs6559527	0.86[JPT][hapmap]
rs7043451	0.84[JPT][hapmap]
rs7044071	0.91[JPT][hapmap]
rs7046199	0.85[JPT][hapmap]
rs7357615	0.85[JPT][hapmap]
rs7856778	0.86[JPT][hapmap]
rs7866250	0.92[JPT][hapmap]
rs885174	0.86[ASN][1000 genomes]
rs932967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2757340	chr9:72018246-72048098	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2759694	chr9:72018246-72048098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv893432	chr9:72028323-72056397	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1047666	chr9:72028458-72049592	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2761289	chr9:72028470-72049604	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1049763	chr9:72029588-72049592	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2422080	chr9:72029600-72049028	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1045274	chr9:72032381-72049592	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1048256	chr9:72032381-72067786	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1045239	chr9:72032381-72067942	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1041436	chr9:72032381-72069314	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv3396573	chr9:72033229-72054457	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv3483546	chr9:72034132-72038630	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3483547	chr9:72034132-72038630	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv15039	chr9:72034725-72049025	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv2761532	chr9:72035189-72049604	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv442554	chr9:72035193-72049028	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1038185	chr9:72035199-72057304	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv3693030	chr9:72035847-72048477	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv520760	chr9:72035847-72048477	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv818703	chr9:72035847-72048477	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11138566	C9orf57	cis	cerebellum	SCAN
rs11138566	KLF9	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72027000-72040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:72036000-72037600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:72036200-72043000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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