Variant report

Variant	rs17078944
Chromosome Location	chr3:46580591-46580592
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11713015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1402152	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1520493	0.87[ASN][1000 genomes]
rs2373255	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34667937	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801759	0.82[ASN][1000 genomes]
rs7632776	0.83[AFR][1000 genomes]
rs939421	0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9848648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876737	chr3:46569721-46595431	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17078944	TDGF1	cis	lung	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
2	chr3:46549200-46585400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:46556400-46591000	Weak transcription	Psoas Muscle	Psoas
4	chr3:46558400-46591000	Weak transcription	Gastric	stomach
5	chr3:46567200-46586000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:46569000-46584200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:46571000-46583800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:46571600-46587000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:46577400-46580600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:46577400-46581600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:46577600-46580600	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:46577600-46581600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:46577800-46580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:46578400-46580600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:46578400-46580600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:46578400-46581000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:46578400-46581600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:46578400-46599200	Weak transcription	HSMMtube	muscle
19	chr3:46578800-46581200	Weak transcription	Right Ventricle	heart
20	chr3:46578800-46586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:46579000-46581000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:46579000-46581600	Enhancers	NHDF-Ad	bronchial
23	chr3:46579000-46583000	Weak transcription	Ovary	ovary
24	chr3:46579200-46580600	Flanking Active TSS	GM12878-XiMat	blood
25	chr3:46579200-46581800	Flanking Active TSS	Dnd41	blood
26	chr3:46579200-46587800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:46579400-46580600	Genic enhancers	Left Ventricle	heart
28	chr3:46579400-46580800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:46579400-46581000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:46579400-46581600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:46579400-46581600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:46579600-46581200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:46579600-46584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:46579800-46581000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:46579800-46581400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:46579800-46581400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr3:46579800-46586200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:46580000-46580800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:46580000-46580800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:46580000-46580800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:46580000-46580800	Enhancers	NHEK	skin
42	chr3:46580000-46581200	Weak transcription	Colonic Mucosa	Colon
43	chr3:46580000-46581400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr3:46580000-46581400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr3:46580000-46581400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:46580000-46581600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr3:46580000-46581600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr3:46580200-46580600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:46580200-46580600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:46580200-46580600	Enhancers	Fetal Muscle Leg	muscle

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