Variant report

Variant	rs7173670
Chromosome Location	chr15:77454235-77454236
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1015813	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519158	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853625	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853633	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854182	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854466	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856513	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856538	0.90[ASN][1000 genomes]
rs11857804	0.85[EUR][1000 genomes]
rs12324366	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900110	0.86[ASN][1000 genomes]
rs12902106	0.83[ASN][1000 genomes]
rs12902434	0.83[ASN][1000 genomes]
rs12902446	0.89[ASN][1000 genomes]
rs13379686	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13380152	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374201	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1446313	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17381652	0.89[ASN][1000 genomes]
rs17381821	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17383078	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17466480	0.91[ASN][1000 genomes]
rs17468413	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867780	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044453	0.89[ASN][1000 genomes]
rs2137977	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292594	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2864079	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34572155	0.82[ASN][1000 genomes]
rs35093280	0.89[ASN][1000 genomes]
rs4638539	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886514	0.84[ASN][1000 genomes]
rs4886852	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886857	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55881066	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55994208	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56070388	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58792939	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59831220	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60079927	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60761381	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60863150	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182221	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74025074	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74025104	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74025105	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74027548	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74027549	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7496431	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs7173670	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
2	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
3	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
4	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:77438400-77461000	Weak transcription	NH-A	brain
6	chr15:77438600-77457600	Weak transcription	Gastric	stomach
7	chr15:77438600-77461400	Weak transcription	Aorta	Aorta
8	chr15:77438600-77469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:77438600-77470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:77439800-77460600	Weak transcription	HSMMtube	muscle
11	chr15:77444200-77460600	Weak transcription	NHEK	skin
12	chr15:77445200-77461000	Weak transcription	Small Intestine	intestine
13	chr15:77446400-77454600	Weak transcription	Esophagus	oesophagus
14	chr15:77447800-77456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:77448200-77457400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:77449000-77465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:77450000-77455200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:77450000-77458000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:77450000-77460600	Weak transcription	Left Ventricle	heart
20	chr15:77450400-77471200	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:77450600-77471200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:77450800-77454600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:77450800-77471200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:77451000-77454600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:77451000-77454800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:77451000-77455000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:77451000-77456200	Weak transcription	Psoas Muscle	Psoas
28	chr15:77451000-77466000	Weak transcription	Brain Substantia Nigra	brain
29	chr15:77451000-77468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:77451000-77470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:77451000-77470800	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:77451000-77471200	Weak transcription	HSMM	muscle
33	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:77451200-77460200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:77451200-77466000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:77451200-77471800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:77451400-77457200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:77451400-77471200	Weak transcription	NHDF-Ad	bronchial
40	chr15:77451600-77454800	Enhancers	Fetal Intestine Large	intestine
41	chr15:77451600-77456200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:77451600-77458000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:77452000-77456200	Enhancers	Primary B cells from cord blood	blood
44	chr15:77452200-77454800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr15:77452200-77456400	Enhancers	Primary B cells from peripheral blood	blood
46	chr15:77452200-77458400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:77452400-77454800	Enhancers	Pancreas	Pancrea
48	chr15:77452400-77469000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:77453000-77460800	Weak transcription	Lung	lung
50	chr15:77453200-77454600	Enhancers	HUES48 Cell Line	embryonic stem cell

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