Variant report

Variant	rs10756664
Chromosome Location	chr9:15433876-15433877
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	SPI1	chr9:15433688-15434001	GM12891	blood:	n/a	n/a
2	SPI1	chr9:15433665-15434036	GM12891	blood:	n/a	n/a
3	RUNX3	chr9:15433617-15434173	GM12878	blood:	n/a	n/a
4	RUNX3	chr9:15433623-15434163	GM12878	blood:	n/a	n/a
5	SPI1	chr9:15433781-15434002	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-319P	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10081655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10115540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117968	0.94[CHB][hapmap]
rs1033056	0.81[CHB][hapmap]
rs10481556	0.89[EUR][1000 genomes]
rs10511611	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs10733292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10738392	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10738393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10738395	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs10738397	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10756663	0.88[EUR][1000 genomes]
rs10756665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756666	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10756667	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756668	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756669	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10962036	0.83[ASN][1000 genomes]
rs1123038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12093	0.83[ASW][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs13248	1.00[ASW][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1397214	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1397215	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs16933311	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs16933316	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1976599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1983207	0.83[EUR][1000 genomes]
rs2136710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2175258	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2175259	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2382529	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2665504	0.82[ASW][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2737829	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2737831	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2737835	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs2737842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4741498	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4741500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4741501	1.00[JPT][hapmap]
rs4741503	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4741504	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4741505	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4741506	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4741507	0.94[JPT][hapmap]
rs4741508	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs60046377	0.82[AFR][1000 genomes]
rs6474915	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6474916	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6474918	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6474923	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7021042	0.94[JPT][hapmap]
rs7023290	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026910	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7026970	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7029985	0.85[EUR][1000 genomes]
rs7034447	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7042165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7046713	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7470309	0.88[ASN][1000 genomes]
rs7470323	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7857850	0.87[ASN][1000 genomes]
rs907075	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs907076	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9650682	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9650683	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][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	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	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	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
rs10756664	SNAPC3	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15423600-15434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:15423600-15439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:15425000-15437000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:15425400-15439000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:15425800-15434000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:15426200-15441800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:15426400-15434000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:15426400-15435400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:15426400-15436000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:15426400-15439000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:15426400-15439800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:15426400-15441800	Weak transcription	Spleen	Spleen
15	chr9:15426400-15442800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:15426400-15443600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:15426400-15443600	Weak transcription	Gastric	stomach
18	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:15426600-15434000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:15426600-15434000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:15426600-15442400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:15426600-15443400	Weak transcription	Fetal Heart	heart
23	chr9:15426800-15434200	Weak transcription	Fetal Brain Male	brain
24	chr9:15427000-15436000	Weak transcription	Fetal Brain Female	brain
25	chr9:15427000-15443400	Weak transcription	NHEK	skin
26	chr9:15431000-15437600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:15431000-15439000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:15431200-15434000	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:15431200-15439200	Strong transcription	HepG2	liver
30	chr9:15431400-15434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:15431400-15434000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr9:15431400-15434000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:15431400-15434000	Weak transcription	Fetal Stomach	stomach
34	chr9:15431400-15434400	Weak transcription	Brain Germinal Matrix	brain
35	chr9:15431400-15435200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:15431400-15436000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:15431400-15439800	Weak transcription	Hela-S3	cervix
38	chr9:15431400-15441800	Weak transcription	Lung	lung
39	chr9:15431400-15442400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:15431400-15442800	Weak transcription	Brain Angular Gyrus	brain
41	chr9:15431400-15443400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:15431400-15443400	Weak transcription	Pancreas	Pancrea
43	chr9:15431400-15443600	Weak transcription	Aorta	Aorta
44	chr9:15431400-15443600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:15431400-15443600	Weak transcription	Esophagus	oesophagus
46	chr9:15431400-15445800	Weak transcription	Right Ventricle	heart
47	chr9:15431400-15446000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr9:15431400-15447800	Weak transcription	Psoas Muscle	Psoas
49	chr9:15431600-15434400	Strong transcription	K562	blood
50	chr9:15431600-15443400	Weak transcription	Stomach Mucosa	stomach

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