Variant report

Variant	rs10118629
Chromosome Location	chr9:15296450-15296451
allele	A/T
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: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10114494	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10115392	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121612	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10125948	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]
rs10738391	0.82[CHB][hapmap]
rs10810370	0.86[GIH][hapmap];0.88[AMR][1000 genomes]
rs10810373	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs10961957	0.88[AMR][1000 genomes]
rs10961960	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10961963	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10961965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122677	0.81[CEU][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17327373	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2382519	0.88[AMR][1000 genomes]
rs2890998	0.91[GIH][hapmap];0.88[AMR][1000 genomes]
rs4008004	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs491322	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs7022687	0.90[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7023154	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7023864	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10118629	C9orf52	cis	multi-tissue	Pritchard
rs10118629	TTC39B	cis	Lymphoblastoid	GTEx
rs10118629	TTC39B	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15277600-15296800	Weak transcription	Gastric	stomach
2	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:15292200-15296800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:15294200-15296600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:15294600-15297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:15294800-15297000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:15294800-15297200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:15294800-15297600	Enhancers	Lung	lung
13	chr9:15295000-15296800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:15295000-15297000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:15295200-15297800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr9:15295400-15296800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:15295400-15297200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:15295400-15297200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:15295400-15297200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:15295400-15297400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:15295600-15296600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:15295600-15296600	Flanking Active TSS	GM12878-XiMat	blood
23	chr9:15295600-15297400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr9:15295800-15296600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:15295800-15296600	Flanking Active TSS	Fetal Kidney	kidney
26	chr9:15295800-15296800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr9:15295800-15296800	Flanking Active TSS	Fetal Thymus	thymus
28	chr9:15295800-15297000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr9:15295800-15297200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:15295800-15297200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr9:15295800-15297200	Flanking Active TSS	Dnd41	blood
32	chr9:15295800-15297600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr9:15295800-15298400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr9:15296000-15296600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr9:15296000-15296600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr9:15296000-15296600	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr9:15296000-15296600	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr9:15296000-15296600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:15296000-15296600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:15296000-15296600	Active TSS	Brain Substantia Nigra	brain
41	chr9:15296000-15296600	Active TSS	Fetal Muscle Trunk	muscle
42	chr9:15296000-15296600	Active TSS	Fetal Muscle Leg	muscle
43	chr9:15296000-15296600	Flanking Active TSS	Fetal Stomach	stomach
44	chr9:15296000-15296600	Weak transcription	Spleen	Spleen
45	chr9:15296000-15296600	Active TSS	HSMMtube	muscle
46	chr9:15296000-15296800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:15296000-15296800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:15296000-15296800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr9:15296000-15296800	Active TSS	Aorta	Aorta
50	chr9:15296000-15296800	Active TSS	Brain Angular Gyrus	brain

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