Variant report

Variant	rs2185938
Chromosome Location	chr9:15293427-15293428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15283111..15284924-chr9:15291453..15293765,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10120504	1.00[JPT][hapmap]
rs10122040	1.00[JPT][hapmap]
rs10122202	1.00[JPT][hapmap]
rs10125329	1.00[JPT][hapmap]
rs10810369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10961950	1.00[JPT][hapmap]
rs10961951	1.00[JPT][hapmap]
rs10961955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10962043	1.00[CHB][hapmap]
rs12003180	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1215112	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1475229	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs16933318	1.00[CHB][hapmap]
rs2156109	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616751	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3901749	1.00[JPT][hapmap]
rs3933784	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3933785	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4237138	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs471364	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs486349	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540885	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570524	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585002	0.94[CEU][hapmap]
rs612183	0.82[JPT][hapmap]
rs643531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660686	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675849	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs677578	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686030	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7035671	0.82[JPT][hapmap]
rs7035801	0.82[JPT][hapmap]
rs7037559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7873299	1.00[JPT][hapmap]
rs9657588	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2762797	chr9:15282415-15297028	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv969751	chr9:15287487-15294727	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2185938	C9orf52	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:15277600-15296800	Weak transcription	Gastric	stomach
3	chr9:15278000-15295200	Weak transcription	Pancreas	Pancrea
4	chr9:15283600-15293800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr9:15285200-15293800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:15286800-15293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:15287000-15293600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:15287000-15294200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:15287600-15293600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:15287600-15294000	Weak transcription	Small Intestine	intestine
12	chr9:15288600-15294200	Weak transcription	HepG2	liver
13	chr9:15288800-15293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:15288800-15293800	Weak transcription	Fetal Lung	lung
15	chr9:15288800-15294800	Weak transcription	Lung	lung
16	chr9:15289200-15295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:15290800-15293800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:15290800-15294200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:15291000-15293800	Weak transcription	Stomach Mucosa	stomach
22	chr9:15291200-15294200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:15291200-15296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:15291600-15294200	Weak transcription	Fetal Brain Male	brain
26	chr9:15291800-15293800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr9:15292000-15294000	Weak transcription	Primary B cells from cord blood	blood
28	chr9:15292000-15294200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:15292200-15294600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:15292200-15296000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:15292200-15296800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:15292400-15293600	Weak transcription	Fetal Stomach	stomach
33	chr9:15292400-15294000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:15292600-15295800	Enhancers	HMEC	breast
35	chr9:15292600-15296000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:15292800-15293800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:15292800-15294000	Enhancers	Primary T cells from cord blood	blood
38	chr9:15293000-15293600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr9:15293000-15293800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr9:15293000-15294400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:15293000-15295800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr9:15293000-15295800	Enhancers	NHEK	skin
43	chr9:15293000-15296000	Enhancers	Thymus	Thymus
44	chr9:15293200-15293600	Genic enhancers	Primary hematopoietic stem cells	blood
45	chr9:15293200-15293600	Enhancers	Brain Anterior Caudate	brain
46	chr9:15293200-15293600	Enhancers	Colon Smooth Muscle	Colon
47	chr9:15293200-15293600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:15293200-15293600	Enhancers	Rectal Smooth Muscle	rectum
49	chr9:15293200-15293800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:15293200-15293800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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