Variant report

Variant	rs12339417
Chromosome Location	chr9:15498495-15498496
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	chr9:15494263..15496917-chr9:15497648..15499315,2	K562	blood:
2	chr9:15497676..15499594-chr9:15514470..15516149,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10124624	0.81[ASN][1000 genomes]
rs10283923	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283927	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1033056	0.81[MEX][hapmap]
rs1046388	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10738393	0.83[LWK][hapmap]
rs10738397	0.90[LWK][hapmap];0.81[MKK][hapmap]
rs10756666	0.88[LWK][hapmap]
rs10962048	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12336503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380487	0.82[CHB][hapmap]
rs12683553	0.96[ASN][1000 genomes]
rs12685082	1.00[JPT][hapmap]
rs12686545	0.89[ASN][1000 genomes]
rs13248	0.89[JPT][hapmap]
rs13288118	1.00[CHB][hapmap]
rs13289935	1.00[CHB][hapmap]
rs16933311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16933316	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16933320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs16933348	0.91[ASN][1000 genomes]
rs1828383	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2175257	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277191	0.89[ASN][1000 genomes]
rs2777949	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2777950	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28515581	0.81[EUR][1000 genomes]
rs28537229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4557796	0.83[EUR][1000 genomes]
rs4741508	0.90[LWK][hapmap]
rs55771541	0.87[ASN][1000 genomes]
rs56361298	0.91[ASN][1000 genomes]
rs57467578	0.91[ASN][1000 genomes]
rs58607272	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59639757	0.87[ASN][1000 genomes]
rs62571010	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571022	0.91[ASN][1000 genomes]
rs62571023	0.91[ASN][1000 genomes]
rs62571024	0.91[ASN][1000 genomes]
rs62571027	0.85[ASN][1000 genomes]
rs62571030	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62571031	0.81[ASN][1000 genomes]
rs62571032	0.81[ASN][1000 genomes]
rs6474927	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7018658	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021153	0.85[ASN][1000 genomes]
rs7021778	0.89[JPT][hapmap]
rs73408328	0.91[ASN][1000 genomes]
rs7852774	0.81[ASN][1000 genomes]
rs7856318	0.92[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs7856710	0.81[ASN][1000 genomes]
rs7857933	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7862428	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7863046	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7863139	0.96[ASN][1000 genomes]
rs907076	0.90[LWK][hapmap]

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	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
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12339417	C9orf93	cis	cerebellum	SCAN
rs12339417	C9orf150	cis	cerebellum	SCAN
rs12339417	ADAMTSL1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
2	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
4	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
6	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:15467200-15501000	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:15467400-15505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:15469200-15505600	Weak transcription	NHLF	lung
10	chr9:15472200-15509000	Weak transcription	HMEC	breast
11	chr9:15476400-15504000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:15476600-15508800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:15476600-15510000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:15477000-15504800	Weak transcription	HSMM	muscle
15	chr9:15477000-15509600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:15478000-15505000	Weak transcription	Adipose Nuclei	Adipose
17	chr9:15480200-15505200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:15481600-15509600	Weak transcription	Aorta	Aorta
19	chr9:15482600-15501000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:15483000-15504800	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:15483000-15504800	Weak transcription	Brain Substantia Nigra	brain
22	chr9:15485200-15499200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:15485800-15501000	Weak transcription	HUVEC	blood vessel
24	chr9:15485800-15509800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:15486000-15505000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:15486200-15501600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:15486400-15505800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:15486600-15499000	Weak transcription	NH-A	brain
29	chr9:15486600-15504000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:15486800-15505600	Weak transcription	K562	blood
31	chr9:15488600-15501000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr9:15488600-15502000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:15488800-15505400	Weak transcription	NHDF-Ad	bronchial
34	chr9:15492600-15502000	Weak transcription	Liver	Liver
35	chr9:15492600-15508200	Weak transcription	Brain Angular Gyrus	brain
36	chr9:15492600-15509800	Weak transcription	Colonic Mucosa	Colon
37	chr9:15492800-15499200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr9:15492800-15505800	Weak transcription	Fetal Brain Male	brain
39	chr9:15493000-15499000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:15493000-15500200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:15493000-15500200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:15493000-15500400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:15493000-15500400	Weak transcription	Fetal Stomach	stomach
44	chr9:15493000-15501800	Weak transcription	Left Ventricle	heart
45	chr9:15493000-15502200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:15493000-15502200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:15493000-15502200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:15493000-15502200	Weak transcription	Hela-S3	cervix
49	chr9:15493000-15504400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:15493000-15504600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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