Variant report

Variant	rs13380152
Chromosome Location	chr15:77436386-77436387
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853625	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11853633	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854466	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856538	0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs11857330	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs11857804	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900110	0.83[ASN][1000 genomes]
rs12902446	0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs13379686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374201	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446313	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]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17381652	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17383078	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17466480	0.93[ASN][1000 genomes]
rs17468413	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2137977	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2864079	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs35093280	0.91[ASN][1000 genomes]
rs4592615	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4638539	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886514	0.80[ASN][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886857	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55881066	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56070388	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58792939	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59831220	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60079927	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173670	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025104	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74025105	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7496431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13380152	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
2	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:77419600-77436400	Weak transcription	NHEK	skin
4	chr15:77419600-77449400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:77419800-77436800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:77420400-77436600	Weak transcription	Fetal Heart	heart
7	chr15:77420400-77449800	Weak transcription	Psoas Muscle	Psoas
8	chr15:77421400-77436400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:77426000-77436800	Weak transcription	Ovary	ovary
10	chr15:77426000-77437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:77426000-77437600	Weak transcription	Gastric	stomach
12	chr15:77426000-77449600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
14	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:77426400-77436400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
17	chr15:77428000-77449600	Weak transcription	Primary T cells from cord blood	blood
18	chr15:77432800-77448400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:77433200-77436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:77433200-77436600	Weak transcription	Fetal Lung	lung
21	chr15:77433200-77449200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:77433400-77436400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:77433400-77436600	Weak transcription	Fetal Stomach	stomach
24	chr15:77433400-77449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:77433400-77449400	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:77433400-77449600	Weak transcription	Left Ventricle	heart
27	chr15:77433600-77448400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
29	chr15:77434400-77437000	Weak transcription	HepG2	liver
30	chr15:77434800-77436600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:77434800-77436800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr15:77434800-77438000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:77434800-77449200	Weak transcription	Brain Anterior Caudate	brain
34	chr15:77434800-77449200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:77434800-77449400	Weak transcription	Liver	Liver
36	chr15:77435000-77436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:77435000-77436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:77435000-77438600	Enhancers	Fetal Intestine Small	intestine
39	chr15:77435000-77448400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:77435000-77448600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:77435000-77449200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:77435200-77436400	Enhancers	HSMMtube	muscle
43	chr15:77435200-77439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:77435400-77436400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:77435400-77436400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:77435400-77436400	Enhancers	NHDF-Ad	bronchial
47	chr15:77435400-77436800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:77435400-77437000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:77435400-77437000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr15:77435600-77437400	Strong transcription	Fetal Muscle Trunk	muscle

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