Variant report

Variant	rs9390459
Chromosome Location	chr6:147680359-147680360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1039083	0.83[ASN][1000 genomes]
rs1039084	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1039085	0.83[ASN][1000 genomes]
rs1039086	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1147846	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147847	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12173905	0.86[ASN][1000 genomes]
rs12191720	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12199542	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12527235	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496031	0.94[CHD][hapmap]
rs1496033	0.81[EUR][1000 genomes]
rs1992389	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047286	0.81[EUR][1000 genomes]
rs2328813	0.86[ASN][1000 genomes]
rs2502732	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2582924	0.85[ASN][1000 genomes]
rs2582925	0.80[ASN][1000 genomes]
rs2582929	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2786183	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2786185	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2786187	0.86[ASN][1000 genomes]
rs4896904	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4896905	0.81[EUR][1000 genomes]
rs4896906	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4896907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896908	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs519630	0.83[EUR][1000 genomes]
rs562417	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs566028	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs577877	0.80[ASN][1000 genomes]
rs580657	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs584456	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58987334	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591355	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597631	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs614476	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs617975	0.80[ASN][1000 genomes]
rs618474	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs619626	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620715	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62435617	0.87[ASN][1000 genomes]
rs62435630	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs633603	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656728	0.89[CHB][hapmap]
rs659399	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs673944	0.87[ASN][1000 genomes]
rs6928919	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932613	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7739314	0.94[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762087	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7765526	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769576	0.92[ASN][1000 genomes]
rs9373522	0.92[ASN][1000 genomes]
rs9377048	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9390458	0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs9390460	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390461	0.89[EUR][1000 genomes]
rs9390463	0.96[ASN][1000 genomes]
rs9399597	0.93[ASN][1000 genomes]
rs9399598	0.97[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs9399599	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403852	0.83[EUR][1000 genomes]
rs9497759	0.83[EUR][1000 genomes]
rs995697	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking 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	21 gene(s)	inside rSNPs	diseases
2	nsv470864	chr6:147539165-147709179	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886754	chr6:147539165-147729477	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv604840	chr6:147539165-147730324	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1832155	chr6:147554900-147715464	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv886755	chr6:147577646-147729477	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv886756	chr6:147580697-147729477	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv830839	chr6:147584914-147757264	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv886757	chr6:147591022-147729477	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv1016430	chr6:147662541-147711882	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1022283	chr6:147663541-147700720	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coagulation factor levels	20231535	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9390459	STXBP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147584400-147684600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:147607400-147707400	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:147610200-147700200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:147619200-147690200	Weak transcription	Fetal Heart	heart
5	chr6:147622600-147708200	Weak transcription	Psoas Muscle	Psoas
6	chr6:147626000-147687000	Weak transcription	Lung	lung
7	chr6:147626000-147700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:147626200-147684000	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:147626200-147684000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:147626200-147687200	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:147626200-147707600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:147626400-147700000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:147628200-147687000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:147631400-147707200	Weak transcription	Hela-S3	cervix
15	chr6:147633800-147684400	Weak transcription	Ovary	ovary
16	chr6:147637000-147686800	Weak transcription	A549	lung
17	chr6:147642800-147705000	Weak transcription	HepG2	liver
18	chr6:147643800-147686800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:147644200-147704000	Weak transcription	GM12878-XiMat	blood
20	chr6:147644400-147686600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:147644600-147684400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:147644800-147683600	Weak transcription	Fetal Brain Female	brain
23	chr6:147645200-147682000	Weak transcription	HMEC	breast
24	chr6:147645200-147715000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:147645800-147685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:147649000-147687200	Weak transcription	Right Ventricle	heart
27	chr6:147649000-147705000	Weak transcription	Fetal Brain Male	brain
28	chr6:147649600-147684000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:147649600-147685200	Weak transcription	Fetal Lung	lung
30	chr6:147649600-147703800	Weak transcription	Fetal Stomach	stomach
31	chr6:147649600-147706000	Weak transcription	Fetal Kidney	kidney
32	chr6:147649600-147711800	Weak transcription	Colonic Mucosa	Colon
33	chr6:147649800-147684200	Weak transcription	Placenta	Placenta
34	chr6:147649800-147708000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:147650000-147684400	Weak transcription	HSMMtube	muscle
36	chr6:147650200-147706400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:147654800-147683800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:147655000-147684000	Weak transcription	HUVEC	blood vessel
39	chr6:147655000-147707800	Weak transcription	Esophagus	oesophagus
40	chr6:147667600-147684200	Weak transcription	Liver	Liver
41	chr6:147667600-147684600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:147668200-147698600	Weak transcription	Aorta	Aorta
43	chr6:147668200-147708000	Weak transcription	NHEK	skin
44	chr6:147668600-147682600	Weak transcription	Fetal Thymus	thymus
45	chr6:147669400-147699600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:147669600-147684400	Weak transcription	Left Ventricle	heart
47	chr6:147675000-147688200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:147675000-147688400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:147676200-147684000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:147676800-147684000	Weak transcription	Brain Anterior Caudate	brain

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