Variant report

Variant	rs686030
Chromosome Location	chr9:15304782-15304783
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	chr9:15300090..15302521-chr9:15304681..15306725,2	MCF-7	breast:
2	chr9:15303560..15305523-chr9:15350040..15352891,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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[CHD][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];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1215112	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16933318	1.00[CHB][hapmap]
rs2156109	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2185938	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2616751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3901749	1.00[JPT][hapmap]
rs3933784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3933785	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4237138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs471364	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs486349	0.92[ASN][1000 genomes]
rs540885	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs570524	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578194	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs581080	0.88[CEU][hapmap]
rs612183	0.82[JPT][hapmap]
rs643531	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs660686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677578	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7035671	0.82[JPT][hapmap]
rs7035801	0.82[JPT][hapmap]
rs7037559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7873299	1.00[JPT][hapmap]
rs9657588	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv524849	chr9:15299590-15362057	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs686030	MPDZ	cis	parietal	SCAN
rs686030	C9orf52	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:15296800-15305600	Weak transcription	Left Ventricle	heart
6	chr9:15297000-15305200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr9:15297200-15305600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:15297200-15305600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:15297200-15305600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:15297400-15304800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:15297400-15305200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:15297400-15305600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:15297400-15305600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:15297400-15305600	Weak transcription	NHEK	skin
15	chr9:15297400-15305600	Weak transcription	NHLF	lung
16	chr9:15297400-15306000	Weak transcription	HSMM	muscle
17	chr9:15297600-15305200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:15297600-15305200	Weak transcription	HMEC	breast
19	chr9:15297600-15305400	Weak transcription	Fetal Lung	lung
20	chr9:15297600-15305400	Weak transcription	Osteobl	bone
21	chr9:15297600-15305600	Weak transcription	Adipose Nuclei	Adipose
22	chr9:15297600-15305600	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:15297600-15305600	Weak transcription	Esophagus	oesophagus
24	chr9:15297600-15305600	Weak transcription	Lung	lung
25	chr9:15297600-15305600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:15297600-15305800	Weak transcription	Gastric	stomach
27	chr9:15297600-15305800	Weak transcription	Right Atrium	heart
28	chr9:15297800-15304800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:15297800-15305600	Weak transcription	NHDF-Ad	bronchial
30	chr9:15297800-15306000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:15298000-15305400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:15298200-15305800	Weak transcription	Brain Angular Gyrus	brain
33	chr9:15298600-15305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:15299000-15305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:15299200-15305000	Weak transcription	Fetal Kidney	kidney
36	chr9:15299200-15305400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:15299400-15305200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:15299600-15304800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:15300200-15304800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:15300200-15305600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:15300400-15305400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:15300400-15305600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:15300400-15306000	Weak transcription	HUVEC	blood vessel
44	chr9:15300600-15304800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:15300600-15305000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:15300600-15305200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr9:15300800-15305200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:15300800-15305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:15300800-15305600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:15300800-15305600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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