Variant report

Variant	rs3784788
Chromosome Location	chr15:77759896-77759897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11853696	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857330	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11858844	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324016	0.81[ASN][1000 genomes]
rs12324211	0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912084	0.83[ASN][1000 genomes]
rs13380202	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493699	0.81[ASN][1000 genomes]
rs16968799	0.81[ASN][1000 genomes]
rs16968897	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs17384809	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17385059	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17385352	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17470529	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17470952	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17471252	0.85[ASN][1000 genomes]
rs17471431	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472200	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2012740	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012756	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137111	0.82[JPT][hapmap]
rs2172587	0.81[ASN][1000 genomes]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28437977	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35651077	0.81[ASN][1000 genomes]
rs3784787	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4592615	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs4886863	0.83[ASN][1000 genomes]
rs4886864	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886865	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886874	0.82[JPT][hapmap]
rs56097641	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59204923	0.83[EUR][1000 genomes]
rs59362734	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59386622	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61306472	0.83[EUR][1000 genomes]
rs62007297	0.84[ASN][1000 genomes]
rs62010566	0.81[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs74026910	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026912	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026913	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74026918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74026923	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026925	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74026926	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035526	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883627	0.94[JPT][hapmap]
rs907371	0.82[JPT][hapmap]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[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	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
2	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
3	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
4	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
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3784788	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77743200-77763200	Weak transcription	Brain Germinal Matrix	brain
2	chr15:77748200-77766800	Weak transcription	Aorta	Aorta
3	chr15:77748400-77770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:77749000-77770400	Weak transcription	Spleen	Spleen
5	chr15:77749600-77763400	Weak transcription	Fetal Brain Male	brain
6	chr15:77750000-77760600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:77750000-77763400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:77750000-77766400	Weak transcription	Psoas Muscle	Psoas
9	chr15:77750000-77770400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:77750200-77763400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:77750200-77763800	Weak transcription	Right Ventricle	heart
12	chr15:77750200-77767000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:77750800-77768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:77750800-77768200	Strong transcription	Liver	Liver
19	chr15:77750800-77768200	Strong transcription	Fetal Intestine Large	intestine
20	chr15:77750800-77768400	Strong transcription	Primary T cells from cord blood	blood
21	chr15:77750800-77780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:77751000-77762600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:77751000-77766200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:77751000-77768600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:77751000-77770600	Weak transcription	Gastric	stomach
26	chr15:77751000-77770600	Weak transcription	Right Atrium	heart
27	chr15:77751000-77773600	Weak transcription	Stomach Mucosa	stomach
28	chr15:77752000-77763600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:77752200-77761800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:77752400-77762800	Weak transcription	HepG2	liver
31	chr15:77752800-77760600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:77753400-77777600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:77753600-77766600	Strong transcription	GM12878-XiMat	blood
34	chr15:77754000-77762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:77754000-77767800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:77755000-77768600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:77755200-77762400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:77755200-77768000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:77755200-77775600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:77755400-77760000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:77755400-77760200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:77755400-77766000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:77755400-77768200	Strong transcription	Primary B cells from cord blood	blood
44	chr15:77755400-77777800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:77755600-77765600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:77755600-77766000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:77755600-77766200	Strong transcription	Placenta	Placenta
48	chr15:77755600-77768600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:77755600-77770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:77755800-77762400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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