Variant report

Variant	rs56070388
Chromosome Location	chr15:77557628-77557629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519158	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11853625	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853633	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11854182	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11854466	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856513	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857330	0.85[ASN][1000 genomes]
rs11857804	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148274	0.89[ASN][1000 genomes]
rs12324366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900110	0.83[ASN][1000 genomes]
rs12902106	0.85[ASN][1000 genomes]
rs12902434	0.85[ASN][1000 genomes]
rs12912963	0.89[ASN][1000 genomes]
rs13379686	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13380152	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13380202	0.81[ASN][1000 genomes]
rs1374201	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1446313	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16968730	0.89[ASN][1000 genomes]
rs17381821	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17383078	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17384809	0.81[ASN][1000 genomes]
rs17385059	0.81[ASN][1000 genomes]
rs17385296	0.81[ASN][1000 genomes]
rs17385352	0.81[ASN][1000 genomes]
rs17468413	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867780	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2137977	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292594	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864079	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34572155	0.87[ASN][1000 genomes]
rs4592615	0.85[ASN][1000 genomes]
rs4638539	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886514	0.82[ASN][1000 genomes]
rs4886852	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55881066	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55994208	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58792939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59831220	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60079927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60761381	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60863150	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7163620	0.85[ASN][1000 genomes]
rs7173670	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182221	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74025074	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74025104	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027548	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027549	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7496431	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806326	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv869991	chr15:77545316-77578885	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv976867	chr15:77545319-77570795	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv33934	chr15:77548764-77579524	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56070388	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
2	chr15:77517400-77559000	Weak transcription	Ovary	ovary
3	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
4	chr15:77527000-77559000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:77527000-77576200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:77528800-77559200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:77528800-77571400	Weak transcription	Right Ventricle	heart
8	chr15:77528800-77574400	Weak transcription	HepG2	liver
9	chr15:77528800-77577200	Weak transcription	Spleen	Spleen
10	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:77529200-77561400	Weak transcription	Primary T cells from cord blood	blood
12	chr15:77529400-77558600	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:77529400-77558600	Weak transcription	Lung	lung
14	chr15:77529400-77558800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:77529400-77559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:77529400-77559600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:77529400-77565400	Weak transcription	Dnd41	blood
18	chr15:77529400-77574400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:77541800-77589800	Weak transcription	Fetal Intestine Small	intestine
20	chr15:77542000-77575200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:77542000-77575200	Weak transcription	HUVEC	blood vessel
22	chr15:77542200-77558800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:77542200-77580000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:77544400-77563600	Weak transcription	Pancreas	Pancrea
25	chr15:77544400-77571400	Weak transcription	HSMMtube	muscle
26	chr15:77544400-77581000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:77544600-77558800	Weak transcription	NHLF	lung
28	chr15:77544600-77558800	Weak transcription	Osteobl	bone
29	chr15:77544600-77559000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:77544600-77570200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:77544600-77570800	Weak transcription	Left Ventricle	heart
32	chr15:77544600-77589200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:77544800-77570600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:77545000-77558800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:77545000-77564000	Weak transcription	Primary B cells from cord blood	blood
36	chr15:77545200-77576200	Weak transcription	HSMM	muscle
37	chr15:77548200-77566600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:77552400-77558600	Weak transcription	Fetal Stomach	stomach
39	chr15:77552600-77558600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:77552600-77558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:77552600-77559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:77552600-77567200	Weak transcription	Fetal Lung	lung
43	chr15:77552600-77574200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr15:77553200-77559200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:77553400-77559000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:77553400-77559000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:77553400-77559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:77553400-77573200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:77556200-77561600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:77556800-77559400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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