Variant report

Variant	rs10125948
Chromosome Location	chr9:15294667-15294668
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15293831..15297894-chr9:15305171..15308300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10114494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10118629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10121612	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10738391	0.88[CHB][hapmap]
rs10810370	0.88[AMR][1000 genomes]
rs10810373	0.85[CEU][hapmap]
rs10961957	0.88[AMR][1000 genomes]
rs10961960	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10961963	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10961965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1122677	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17327373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2382519	0.88[AMR][1000 genomes]
rs2890998	0.88[AMR][1000 genomes]
rs4008004	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs491322	0.82[CHB][hapmap]
rs7022687	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7023154	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7023864	0.88[AMR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10125948	C9orf52	cis	multi-tissue	Pritchard
rs10125948	TTC39B	cis	Lymphoblastoid	GTEx
rs10125948	C9orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

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	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:15288800-15294800	Weak transcription	Lung	lung
6	chr9:15289200-15295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:15291200-15296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:15292200-15296000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:15292200-15296800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:15292600-15295800	Enhancers	HMEC	breast
14	chr9:15292600-15296000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr9:15293000-15295800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr9:15293000-15295800	Enhancers	NHEK	skin
17	chr9:15293000-15296000	Enhancers	Thymus	Thymus
18	chr9:15293200-15294800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr9:15293200-15295600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:15293200-15295600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:15293200-15296000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:15293200-15296000	Enhancers	Fetal Intestine Small	intestine
23	chr9:15293400-15294800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr9:15293400-15294800	Enhancers	Aorta	Aorta
25	chr9:15293400-15295000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:15293400-15295400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:15293400-15295600	Enhancers	NHLF	lung
28	chr9:15293400-15295600	Enhancers	Osteobl	bone
29	chr9:15293400-15295800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr9:15293400-15295800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:15293400-15295800	Enhancers	Fetal Thymus	thymus
32	chr9:15293400-15295800	Enhancers	Right Atrium	heart
33	chr9:15293400-15295800	Enhancers	HSMM	muscle
34	chr9:15293400-15296000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr9:15293400-15296400	Enhancers	Fetal Intestine Large	intestine
36	chr9:15293600-15294800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr9:15293600-15295600	Enhancers	Liver	Liver
38	chr9:15293600-15295800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:15293600-15295800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:15293600-15296000	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:15293600-15296000	Enhancers	Fetal Stomach	stomach
42	chr9:15293800-15294800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:15293800-15295400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:15293800-15295800	Enhancers	Duodenum Mucosa	Duodenum
45	chr9:15293800-15295800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr9:15293800-15295800	Enhancers	Stomach Mucosa	stomach
47	chr9:15293800-15296000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:15293800-15296000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr9:15294000-15294800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr9:15294000-15295400	Enhancers	NHDF-Ad	bronchial

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