Variant report

Variant	rs10119532
Chromosome Location	chr9:79088523-79088524
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79073421..79076264-chr9:79087604..79089143,2	MCF-7	breast:
2	chr9:79088287..79091027-chr9:79095591..79098128,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1057406	0.84[MEX][hapmap]
rs10735646	0.82[JPT][hapmap]
rs11144864	0.89[GIH][hapmap]
rs11144865	0.89[GIH][hapmap]
rs11144922	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237420	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344941	0.85[CHB][hapmap]
rs2282683	0.84[MEX][hapmap]
rs3739516	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4526423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4745551	0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[ASN][1000 genomes]
rs4745552	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62565112	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62565119	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019479	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707739	0.84[MEX][hapmap]
rs7465809	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785934	0.91[ASN][1000 genomes]
rs785936	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7862822	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7871849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10119532	VPS13A	cis	cerebellum	SCAN
rs10119532	ZFAND5	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79075400-79089800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:79075400-79090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:79075400-79101000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
5	chr9:79077600-79092800	Weak transcription	Fetal Stomach	stomach
6	chr9:79078600-79092400	Weak transcription	HMEC	breast
7	chr9:79080800-79117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:79081400-79088800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:79081800-79093000	Weak transcription	Lung	lung
10	chr9:79081800-79117200	Weak transcription	Gastric	stomach
11	chr9:79082600-79117600	Weak transcription	NHLF	lung
12	chr9:79083000-79088800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:79083600-79090200	Weak transcription	HSMM	muscle
14	chr9:79083600-79090400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:79083600-79092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:79085200-79089000	Genic enhancers	Osteobl	bone
17	chr9:79085200-79093000	Enhancers	Primary B cells from peripheral blood	blood
18	chr9:79085600-79088600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:79085600-79089000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr9:79085600-79091200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr9:79085800-79088600	Enhancers	Fetal Intestine Large	intestine
22	chr9:79085800-79088800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr9:79085800-79088800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr9:79085800-79089000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:79085800-79089000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr9:79085800-79089000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:79086000-79089000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:79086000-79089000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:79086200-79093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:79086800-79089000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:79086800-79090600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr9:79086800-79092000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr9:79087000-79089000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:79087200-79088800	Enhancers	Primary hematopoietic stem cells	blood
35	chr9:79087200-79088800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:79087200-79089000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr9:79087400-79088600	Weak transcription	Small Intestine	intestine
38	chr9:79087400-79088800	Flanking Active TSS	GM12878-XiMat	blood
39	chr9:79087400-79089000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr9:79087400-79093000	Weak transcription	Fetal Thymus	thymus
41	chr9:79087600-79088600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:79087600-79088800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:79087600-79090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:79087600-79090600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr9:79087600-79117400	Weak transcription	Colonic Mucosa	Colon
46	chr9:79087800-79093200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr9:79088000-79088600	Weak transcription	Fetal Intestine Small	intestine
48	chr9:79088000-79088800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:79088000-79089000	Enhancers	Primary B cells from cord blood	blood
50	chr9:79088000-79090600	Weak transcription	H9 Cell Line	embryonic stem cell

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