Variant report

Variant	rs12906835
Chromosome Location	chr15:79046989-79046990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072787	0.84[CEU][hapmap]
rs11072800	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633152	0.87[ASN][1000 genomes]
rs11852909	0.82[ASN][1000 genomes]
rs12148817	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899201	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12899940	0.95[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs12901228	0.81[ASN][1000 genomes]
rs12904489	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906022	0.80[ASN][1000 genomes]
rs12906165	0.80[ASN][1000 genomes]
rs12906847	0.85[ASN][1000 genomes]
rs12906977	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907207	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907432	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907536	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12910831	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912245	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913779	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917502	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1383634	0.87[ASN][1000 genomes]
rs1383635	0.84[ASN][1000 genomes]
rs1809412	0.95[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs1825086	0.87[ASN][1000 genomes]
rs1904920	0.84[ASN][1000 genomes]
rs1964562	0.81[ASN][1000 genomes]
rs2017091	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017297	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2046143	0.81[ASN][1000 genomes]
rs2219939	0.82[ASN][1000 genomes]
rs2622821	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34019568	0.81[ASN][1000 genomes]
rs3861181	0.84[CEU][hapmap]
rs4886982	0.82[JPT][hapmap]
rs4887074	0.82[JPT][hapmap]
rs4887078	0.95[CEU][hapmap]
rs4887091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887092	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59414039	0.81[ASN][1000 genomes]
rs6495308	0.80[MEX][hapmap]
rs7176070	0.82[EUR][1000 genomes]
rs7177143	0.85[ASN][1000 genomes]
rs7182567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182993	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755998	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8024939	0.85[ASN][1000 genomes]
rs8030090	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030335	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042059	0.80[MEX][hapmap]
rs8042374	0.80[MEX][hapmap]
rs899997	0.95[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12906835	TMED3	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79040600-79060000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:79042800-79055400	Enhancers	Right Ventricle	heart
3	chr15:79043200-79047200	Weak transcription	NHDF-Ad	bronchial
4	chr15:79043400-79048200	Weak transcription	NH-A	brain
5	chr15:79043400-79048600	Weak transcription	Brain Angular Gyrus	brain
6	chr15:79043400-79049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:79043400-79049200	Weak transcription	NHLF	lung
8	chr15:79043400-79049400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:79043400-79049600	Weak transcription	Pancreas	Pancrea
10	chr15:79043600-79048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:79043600-79048600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:79043600-79049600	Weak transcription	Colonic Mucosa	Colon
13	chr15:79043600-79049800	Weak transcription	Fetal Brain Female	brain
14	chr15:79043600-79077800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:79043800-79048000	Weak transcription	Osteobl	bone
16	chr15:79043800-79048600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:79043800-79049200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:79043800-79049600	Weak transcription	Lung	lung
21	chr15:79043800-79052000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:79043800-79053400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:79044000-79047400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:79044000-79048000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:79044000-79048200	Weak transcription	Primary B cells from cord blood	blood
26	chr15:79044000-79048200	Weak transcription	HUVEC	blood vessel
27	chr15:79044000-79048400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:79044000-79049200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:79044000-79049200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:79044000-79049200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:79044000-79049600	Weak transcription	Stomach Mucosa	stomach
32	chr15:79044000-79050000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr15:79044000-79052600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:79044200-79048200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:79044200-79049200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:79044200-79049200	Weak transcription	Fetal Thymus	thymus
37	chr15:79044200-79059000	Enhancers	Fetal Muscle Trunk	muscle
38	chr15:79044400-79049400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr15:79045000-79047200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:79045000-79055800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:79045000-79059000	Enhancers	Fetal Muscle Leg	muscle
42	chr15:79045200-79047800	Enhancers	Adipose Nuclei	Adipose
43	chr15:79045200-79049200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:79045400-79047600	Enhancers	Right Atrium	heart
45	chr15:79045600-79047000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:79045600-79049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:79046000-79049200	Enhancers	HSMM	muscle
48	chr15:79046200-79047000	Enhancers	Fetal Kidney	kidney
49	chr15:79046200-79047400	Bivalent Enhancer	HepG2	liver
50	chr15:79046200-79047600	Enhancers	Left Ventricle	heart

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