Variant report

Variant	rs4638539
Chromosome Location	chr15:77468338-77468339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519158	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853625	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854466	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11856513	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856538	0.88[ASN][1000 genomes]
rs11857804	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324366	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[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[ASN][1000 genomes]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13380152	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1374201	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1446313	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968730	0.82[ASN][1000 genomes]
rs17381652	0.87[ASN][1000 genomes]
rs17381821	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17383078	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17466480	0.89[ASN][1000 genomes]
rs17468413	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1867780	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044453	0.87[ASN][1000 genomes]
rs2137977	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292594	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864079	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34572155	0.83[ASN][1000 genomes]
rs35093280	0.87[ASN][1000 genomes]
rs4886514	0.85[ASN][1000 genomes]
rs4886852	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886857	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55881066	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56070388	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58792939	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59831220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60079927	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173670	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182221	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74025104	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025105	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[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
rs4638539	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:77438600-77469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:77438600-77470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:77450400-77471200	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:77450600-77471200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:77450800-77471200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:77451000-77468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:77451000-77470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:77451000-77470800	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:77451000-77471200	Weak transcription	HSMM	muscle
11	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:77451200-77471800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:77451400-77471200	Weak transcription	NHDF-Ad	bronchial
15	chr15:77452400-77469000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:77454000-77470000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:77454000-77471200	Weak transcription	NHLF	lung
18	chr15:77454000-77472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:77454200-77469600	Weak transcription	HUVEC	blood vessel
20	chr15:77454200-77471200	Weak transcription	Placenta	Placenta
21	chr15:77454800-77471200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:77456400-77471800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:77456600-77470800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:77456600-77471400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:77456600-77471600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:77457200-77471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:77457200-77475200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:77457200-77475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:77457800-77471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:77458200-77471200	Weak transcription	Spleen	Spleen
31	chr15:77459200-77468800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:77460000-77470200	Weak transcription	Primary B cells from cord blood	blood
33	chr15:77460800-77471200	Weak transcription	Fetal Lung	lung
34	chr15:77460800-77479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:77461200-77471200	Weak transcription	Right Ventricle	heart
36	chr15:77461400-77469800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:77461400-77471200	Weak transcription	Fetal Stomach	stomach
38	chr15:77461600-77471000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:77461600-77471200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:77461600-77471200	Weak transcription	Aorta	Aorta
41	chr15:77461600-77471200	Weak transcription	Left Ventricle	heart
42	chr15:77461600-77471800	Weak transcription	HSMMtube	muscle
43	chr15:77461600-77496800	Weak transcription	Lung	lung
44	chr15:77461800-77468600	Weak transcription	Osteobl	bone
45	chr15:77461800-77469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:77461800-77470600	Weak transcription	Fetal Heart	heart
47	chr15:77461800-77470800	Weak transcription	Primary T cells from cord blood	blood
48	chr15:77461800-77472400	Weak transcription	NH-A	brain
49	chr15:77465200-77477000	Weak transcription	Gastric	stomach
50	chr15:77465400-77469000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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