Variant report

Variant	rs12902446
Chromosome Location	chr15:77439144-77439145
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77432535..77435036-chr15:77437299..77439209,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10519158	0.87[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs11853633	0.89[ASN][1000 genomes]
rs11854182	0.89[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11856538	0.92[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857330	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12148274	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12324366	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs12900110	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902106	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902434	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912963	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13379686	0.93[ASN][1000 genomes]
rs13380152	0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1446313	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16968730	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17381652	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17381821	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17383078	0.85[ASN][1000 genomes]
rs17466480	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1867780	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2044453	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs34572155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35093280	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4592615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4638539	0.87[ASN][1000 genomes]
rs4886514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886852	0.87[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs59831220	0.89[ASN][1000 genomes]
rs7163620	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173670	0.89[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs74025074	0.93[ASN][1000 genomes]
rs7496431	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9806326	0.81[AMR][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
rs12902446	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
2	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:77419600-77449400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:77420400-77449800	Weak transcription	Psoas Muscle	Psoas
5	chr15:77426000-77449600	Weak transcription	Brain Angular Gyrus	brain
6	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
7	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
9	chr15:77428000-77449600	Weak transcription	Primary T cells from cord blood	blood
10	chr15:77432800-77448400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:77433200-77449200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:77433400-77449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:77433400-77449400	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:77433400-77449600	Weak transcription	Left Ventricle	heart
15	chr15:77433600-77448400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
17	chr15:77434800-77449200	Weak transcription	Brain Anterior Caudate	brain
18	chr15:77434800-77449200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:77434800-77449400	Weak transcription	Liver	Liver
20	chr15:77435000-77448400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:77435000-77448600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:77435000-77449200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:77435200-77439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:77436000-77439800	Enhancers	Stomach Mucosa	stomach
25	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
26	chr15:77436200-77449000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:77436200-77449400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:77436800-77439400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:77436800-77440800	Enhancers	HSMM	muscle
30	chr15:77436800-77449400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:77437000-77439400	Enhancers	NHLF	lung
32	chr15:77437000-77439600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:77437000-77439600	Weak transcription	Fetal Kidney	kidney
34	chr15:77437000-77439800	Enhancers	HSMMtube	muscle
35	chr15:77437000-77440200	Enhancers	Osteobl	bone
36	chr15:77437000-77440800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:77437000-77440800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr15:77437000-77440800	Enhancers	NHDF-Ad	bronchial
39	chr15:77437000-77441000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:77437000-77448800	Weak transcription	Fetal Lung	lung
41	chr15:77437000-77449600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr15:77437000-77451600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:77437000-77451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:77437200-77448400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:77437400-77448400	Weak transcription	Fetal Stomach	stomach
47	chr15:77437400-77448600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr15:77437400-77449400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:77437600-77449200	Weak transcription	HUVEC	blood vessel
50	chr15:77437600-77449600	Weak transcription	Fetal Muscle Leg	muscle

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