Variant report

Variant	rs7046713
Chromosome Location	chr9:15458921-15458922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10081655	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10115540	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10117968	0.87[CHB][hapmap]
rs1033056	0.87[CHB][hapmap]
rs10481556	0.84[EUR][1000 genomes]
rs10733292	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10738392	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10738393	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10738395	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10738397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10756663	0.83[EUR][1000 genomes]
rs10756664	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]
rs10756665	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10756667	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756668	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756669	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123038	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12093	0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1397214	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1397215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16933320	0.85[LWK][hapmap]
rs1976599	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1983207	0.88[EUR][1000 genomes]
rs2136710	0.91[EUR][1000 genomes]
rs2175258	0.91[EUR][1000 genomes]
rs2175259	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2382529	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2382530	0.82[ASN][1000 genomes]
rs2665504	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2737829	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs2737831	0.85[EUR][1000 genomes]
rs2737835	1.00[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs2737837	0.84[EUR][1000 genomes]
rs2737842	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4510952	0.85[ASN][1000 genomes]
rs4510953	0.82[ASN][1000 genomes]
rs4741498	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4741500	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4741501	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4741502	0.86[ASN][1000 genomes]
rs4741503	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4741505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4741506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4741507	0.94[JPT][hapmap]
rs4741508	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6474915	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs6474916	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6474918	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6474923	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021042	0.94[JPT][hapmap]
rs7023290	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7026910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7026970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034447	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7040353	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042165	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7470309	0.98[ASN][1000 genomes]
rs7470323	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857850	0.93[ASN][1000 genomes]
rs907075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs907076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9650682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9650683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7046713	SNAPC3	cis	multi-tissue	Pritchard

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	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15434000-15464000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:15438400-15469800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr9:15438800-15468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:15442000-15463000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:15442200-15469400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr9:15442400-15464400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
13	chr9:15443000-15462400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:15443000-15463800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr9:15443000-15470200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:15443200-15460000	Strong transcription	NH-A	brain
19	chr9:15443200-15460600	Strong transcription	Primary B cells from cord blood	blood
20	chr9:15443200-15465600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:15443200-15469200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:15443200-15478000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:15443400-15466400	Strong transcription	HSMM	muscle
27	chr9:15443400-15467400	Strong transcription	Fetal Brain Female	brain
28	chr9:15443400-15469000	Strong transcription	Osteobl	bone
29	chr9:15443400-15469600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:15443400-15469600	Strong transcription	Fetal Intestine Large	intestine
31	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:15443600-15460200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:15443600-15461800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:15443600-15469000	Strong transcription	Liver	Liver
35	chr9:15443600-15470400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:15444000-15462800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:15444000-15467400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
43	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:15445400-15468600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:15446800-15468200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:15447400-15469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:15448200-15460400	Weak transcription	Esophagus	oesophagus
50	chr9:15448200-15466000	Weak transcription	Gastric	stomach

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