Variant report

Variant	rs10756666
Chromosome Location	chr9:15446868-15446869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:15446682-15446946	K562	blood:	n/a	n/a

Variant related genes	Relation type
SNAPC3	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10081655	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10115540	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10117968	0.87[CHB][hapmap];0.91[MKK][hapmap]
rs1033056	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1046388	0.88[AFR][1000 genomes]
rs10733292	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10738392	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10738393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10738395	0.84[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10738397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10738398	0.85[AFR][1000 genomes]
rs10756664	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10756667	0.85[ASN][1000 genomes]
rs10756669	0.85[ASN][1000 genomes]
rs10962036	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10962039	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1123038	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12093	0.88[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs12339417	0.88[LWK][hapmap]
rs1397214	0.87[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap]
rs1397215	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1976599	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2175259	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2382530	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2665504	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2737829	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2737835	0.80[JPT][hapmap]
rs2737842	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2777950	1.00[ASW][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4510953	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4741500	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs4741501	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741502	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4741503	0.85[ASN][1000 genomes]
rs4741504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4741505	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4741506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4741507	0.89[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4741508	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6474915	0.81[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs6474916	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6474918	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6474923	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7021042	0.89[CEU][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7023290	0.82[ASN][1000 genomes]
rs7026910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026970	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7037580	0.86[AFR][1000 genomes]
rs7042165	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7046713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7470309	0.86[ASN][1000 genomes]
rs7470323	0.86[ASN][1000 genomes]
rs7857850	0.82[ASN][1000 genomes]
rs7862428	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs907075	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9650682	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9650683	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][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	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	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10756666	C9orf150	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:15431400-15447800	Weak transcription	Psoas Muscle	Psoas
3	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15434000-15464000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:15438400-15447800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:15438400-15469800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr9:15438800-15468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:15439400-15447600	Weak transcription	Small Intestine	intestine
10	chr9:15441600-15449400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:15441800-15449000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:15441800-15449800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:15441800-15449800	Strong transcription	Lung	lung
14	chr9:15441800-15457000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:15442000-15449400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:15442000-15458600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:15442000-15463000	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:15442200-15469400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr9:15442400-15449800	Strong transcription	Fetal Stomach	stomach
20	chr9:15442400-15451800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:15442400-15464400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:15442600-15448600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:15442600-15455200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr9:15442600-15455200	Strong transcription	Dnd41	blood
25	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:15442800-15448200	Strong transcription	Spleen	Spleen
28	chr9:15442800-15450200	Strong transcription	Brain Angular Gyrus	brain
29	chr9:15442800-15451000	Strong transcription	Thymus	Thymus
30	chr9:15442800-15453400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:15442800-15456200	Strong transcription	Fetal Muscle Leg	muscle
32	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
33	chr9:15443000-15455400	Strong transcription	Adipose Nuclei	Adipose
34	chr9:15443000-15457000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr9:15443000-15462400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:15443000-15463800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr9:15443000-15470200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:15443200-15448800	Strong transcription	Primary T cells from cord blood	blood
41	chr9:15443200-15448800	Strong transcription	Brain Anterior Caudate	brain
42	chr9:15443200-15449600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:15443200-15450000	Strong transcription	Colonic Mucosa	Colon
44	chr9:15443200-15450000	Strong transcription	Fetal Intestine Small	intestine
45	chr9:15443200-15455200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:15443200-15455400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr9:15443200-15456600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:15443200-15456600	Strong transcription	Placenta	Placenta
49	chr9:15443200-15460000	Strong transcription	NH-A	brain
50	chr9:15443200-15460600	Strong transcription	Primary B cells from cord blood	blood

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