Variant report

Variant	rs10738391
Chromosome Location	chr9:15293579-15293580
allele	C/T
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: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10114494	0.89[CHB][hapmap]
rs10115392	0.82[CHB][hapmap]
rs10118629	0.82[CHB][hapmap]
rs10125948	0.88[CHB][hapmap]
rs10810372	0.88[CEU][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10810373	0.91[ASN][1000 genomes]
rs10961959	0.81[CEU][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10961962	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10961965	0.82[CHB][hapmap]
rs11794919	0.89[AFR][1000 genomes]
rs1215114	0.80[ASN][1000 genomes]
rs17327373	0.88[CHB][hapmap]
rs4008004	0.82[CHB][hapmap]
rs4087078	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4740607	0.81[AMR][1000 genomes]
rs4741483	0.87[AFR][1000 genomes]
rs4741484	0.88[CEU][hapmap]
rs570474	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571888	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635376	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs6474902	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9657569	0.84[CEU][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
rs10738391	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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