Variant report

Variant	rs4886852
Chromosome Location	chr15:77417173-77417174
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10162742	0.83[YRI][hapmap]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853625	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11853633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854466	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856538	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11857330	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs11857804	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900110	0.83[ASN][1000 genomes]
rs12902446	0.87[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs13379686	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380152	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]
rs1374201	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs17381652	0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17383078	1.00[AFR][1000 genomes];0.89[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];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];1.00[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];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2864079	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs35093280	0.91[ASN][1000 genomes]
rs4592615	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4638539	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886514	0.80[ASN][1000 genomes]
rs4886857	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55881066	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56070388	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58792939	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59831220	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60079927	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];0.90[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];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025104	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74025105	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7496431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[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
rs4886852	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77400200-77424200	Weak transcription	Esophagus	oesophagus
2	chr15:77400200-77427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77400200-77429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77400400-77428600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:77400600-77425400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
7	chr15:77404200-77430800	Weak transcription	Thymus	Thymus
8	chr15:77404600-77419200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:77404600-77435600	Weak transcription	HMEC	breast
10	chr15:77407400-77422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:77407400-77422800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:77407400-77422800	Weak transcription	HepG2	liver
13	chr15:77407400-77424000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:77407400-77424400	Weak transcription	Aorta	Aorta
15	chr15:77407400-77425200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:77407400-77425200	Weak transcription	Liver	Liver
17	chr15:77407400-77425200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:77407400-77425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:77407400-77425400	Weak transcription	Gastric	stomach
20	chr15:77407600-77419400	Weak transcription	Psoas Muscle	Psoas
21	chr15:77407600-77420600	Weak transcription	Spleen	Spleen
22	chr15:77407600-77422600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:77407600-77424000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:77407600-77424000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:77407600-77424200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77407600-77424200	Weak transcription	Lung	lung
27	chr15:77407600-77425000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr15:77407600-77425200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr15:77407800-77425000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:77407800-77425400	Weak transcription	Pancreas	Pancrea
31	chr15:77408000-77419200	Weak transcription	Fetal Intestine Large	intestine
32	chr15:77408200-77419400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:77408200-77424000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:77411400-77427000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:77411400-77427400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:77411800-77417800	Weak transcription	Primary T cells from cord blood	blood
37	chr15:77411800-77418000	Weak transcription	Fetal Intestine Small	intestine
38	chr15:77411800-77419000	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:77411800-77419200	Weak transcription	Stomach Mucosa	stomach
40	chr15:77411800-77419400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:77411800-77419400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:77411800-77419400	Weak transcription	Brain Substantia Nigra	brain
43	chr15:77411800-77419600	Weak transcription	Fetal Lung	lung
44	chr15:77411800-77420200	Weak transcription	Left Ventricle	heart
45	chr15:77411800-77420400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:77411800-77424200	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:77411800-77424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:77411800-77425200	Weak transcription	Dnd41	blood
49	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:77412000-77419000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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