Variant report

Variant	rs3743068
Chromosome Location	chr15:79047285-79047286
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12439049	0.83[EUR][1000 genomes]
rs2291196	0.89[EUR][1000 genomes]
rs3743065	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3861181	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4887091	0.84[CEU][hapmap]
rs57224848	0.89[EUR][1000 genomes]
rs59888683	0.90[EUR][1000 genomes]
rs59934757	0.90[EUR][1000 genomes]
rs7176492	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177143	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7182567	0.81[ASW][hapmap];0.85[CEU][hapmap]
rs8024939	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3743068	TMED3	cis	parietal	SCAN
rs3743068	ADAMTS18	trans	brain	seeQTL
rs3743068	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs3743068	ADAMTS5	trans	brain	seeQTL
rs3743068	DPF3	trans	brain	seeQTL
rs3743068	CHAD	trans	brain	seeQTL
rs3743068	KIAA1024	cis	brain	seeQTL

Chromatin state (count:62 , 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	chr15:79043400-79048200	Weak transcription	NH-A	brain
4	chr15:79043400-79048600	Weak transcription	Brain Angular Gyrus	brain
5	chr15:79043400-79049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:79043400-79049200	Weak transcription	NHLF	lung
7	chr15:79043400-79049400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:79043400-79049600	Weak transcription	Pancreas	Pancrea
9	chr15:79043600-79048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:79043600-79048600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:79043600-79049600	Weak transcription	Colonic Mucosa	Colon
12	chr15:79043600-79049800	Weak transcription	Fetal Brain Female	brain
13	chr15:79043600-79077800	Weak transcription	Brain Germinal Matrix	brain
14	chr15:79043800-79048000	Weak transcription	Osteobl	bone
15	chr15:79043800-79048600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:79043800-79049200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:79043800-79049600	Weak transcription	Lung	lung
20	chr15:79043800-79052000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:79043800-79053400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:79044000-79047400	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:79044000-79048000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:79044000-79048200	Weak transcription	Primary B cells from cord blood	blood
25	chr15:79044000-79048200	Weak transcription	HUVEC	blood vessel
26	chr15:79044000-79048400	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:79044000-79049200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:79044000-79049200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:79044000-79049200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:79044000-79049600	Weak transcription	Stomach Mucosa	stomach
31	chr15:79044000-79050000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:79044000-79052600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:79044200-79048200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:79044200-79049200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:79044200-79049200	Weak transcription	Fetal Thymus	thymus
36	chr15:79044200-79059000	Enhancers	Fetal Muscle Trunk	muscle
37	chr15:79044400-79049400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:79045000-79055800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:79045000-79059000	Enhancers	Fetal Muscle Leg	muscle
40	chr15:79045200-79047800	Enhancers	Adipose Nuclei	Adipose
41	chr15:79045200-79049200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr15:79045400-79047600	Enhancers	Right Atrium	heart
43	chr15:79045600-79049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:79046000-79049200	Enhancers	HSMM	muscle
45	chr15:79046200-79047400	Bivalent Enhancer	HepG2	liver
46	chr15:79046200-79047600	Enhancers	Left Ventricle	heart
47	chr15:79046200-79049200	Weak transcription	Spleen	Spleen
48	chr15:79046200-79054600	Enhancers	Fetal Heart	heart
49	chr15:79046400-79063200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:79046600-79047400	Enhancers	Ovary	ovary

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