Variant report

Variant	rs1446313
Chromosome Location	chr15:77475380-77475381
allele	G/T
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	POU2F2	chr15:77475358-77475758	GM12878	blood:	n/a	chr15:77475588-77475601
2	IRF3	chr15:77475372-77475432	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PEAK1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10162742	0.85[YRI][hapmap]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853633	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854466	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856538	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11857330	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs11857804	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900110	0.88[ASN][1000 genomes]
rs12902106	0.85[ASN][1000 genomes]
rs12902434	0.85[ASN][1000 genomes]
rs12902446	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13380152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1374201	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17381652	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17383078	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17466480	0.89[ASN][1000 genomes]
rs17468413	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2137977	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864079	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35093280	0.87[ASN][1000 genomes]
rs4592615	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs4638539	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886514	0.85[ASN][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886857	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55881066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56070388	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58792939	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59831220	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60079927	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173670	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74025104	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025105	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1446313	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:77457200-77475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:77460800-77479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:77461600-77496800	Weak transcription	Lung	lung
6	chr15:77465200-77477000	Weak transcription	Gastric	stomach
7	chr15:77465400-77488200	Weak transcription	Psoas Muscle	Psoas
8	chr15:77466200-77479000	Weak transcription	Brain Anterior Caudate	brain
9	chr15:77466200-77479400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:77467200-77491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:77468600-77475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:77469000-77480200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:77469400-77483800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:77469800-77491200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:77469800-77499200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:77470400-77475600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:77471000-77479000	Weak transcription	Brain Angular Gyrus	brain
18	chr15:77471000-77482600	Weak transcription	Fetal Brain Male	brain
19	chr15:77471200-77475400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:77471400-77475400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr15:77471400-77505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:77471600-77479200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:77471600-77481600	Weak transcription	Pancreas	Pancrea
24	chr15:77471800-77481400	Weak transcription	Spleen	Spleen
25	chr15:77471800-77482000	Weak transcription	Colonic Mucosa	Colon
26	chr15:77471800-77491400	Weak transcription	Aorta	Aorta
27	chr15:77472000-77479200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:77472000-77479200	Weak transcription	NHLF	lung
29	chr15:77472200-77475800	Enhancers	Primary T cells from cord blood	blood
30	chr15:77472200-77476200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:77472200-77479200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:77472200-77479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:77472200-77480000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:77472400-77500800	Weak transcription	HSMMtube	muscle
35	chr15:77472600-77476600	Weak transcription	Stomach Mucosa	stomach
36	chr15:77472800-77477200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:77472800-77477400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:77472800-77477600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:77472800-77479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:77472800-77480000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:77473000-77475800	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:77473000-77476200	Weak transcription	HepG2	liver
43	chr15:77473000-77478600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:77473000-77483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:77473200-77477800	Weak transcription	Brain Substantia Nigra	brain
46	chr15:77473200-77477800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:77473200-77478400	Weak transcription	Fetal Intestine Large	intestine
48	chr15:77473400-77477800	Weak transcription	Fetal Lung	lung
49	chr15:77473400-77479200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:77473400-77479200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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