Variant report

Variant	rs6783573
Chromosome Location	chr3:46600520-46600521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46529825..46532011-chr3:46599266..46600570,56	K562	blood:
2	chr3:46599422..46601505-chr3:46601570..46603414,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1049667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096172	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806701	1.00[ASN][1000 genomes]
rs3806702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs3806703	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769392	1.00[ASN][1000 genomes]
rs7650998	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs939408	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9682509	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6783573	TDGF1	cis	Nerve Tibial	GTEx
rs6783573	TDGF1	cis	lung	GTEx
rs6783573	TDGF1	cis	Heart Left Ventricle	GTEx
rs6783573	TDGF1	cis	Muscle Skeletal	GTEx
rs6783573	TDGF1	cis	Esophagus Muscularis	GTEx
rs6783573	TDGF1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46591800-46606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:46598400-46601000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr3:46599000-46601200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:46599200-46600800	Enhancers	Fetal Heart	heart
5	chr3:46599400-46600600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:46599400-46600600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:46599600-46600600	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr3:46599800-46600600	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr3:46599800-46600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:46599800-46600600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:46599800-46600600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:46599800-46600600	Active TSS	A549	lung
13	chr3:46599800-46601000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:46599800-46601000	Flanking Active TSS	NHEK	skin
15	chr3:46600000-46600600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:46600000-46600600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:46600000-46600600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:46600000-46600600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr3:46600000-46600600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:46600000-46600600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:46600000-46600600	Active TSS	Brain Hippocampus Middle	brain
22	chr3:46600000-46600600	Active TSS	Duodenum Mucosa	Duodenum
23	chr3:46600000-46600600	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr3:46600000-46600600	Active TSS	Fetal Intestine Small	intestine
25	chr3:46600000-46600600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:46600000-46600600	Active TSS	Fetal Muscle Trunk	muscle
27	chr3:46600000-46600600	Flanking Active TSS	Fetal Thymus	thymus
28	chr3:46600000-46600600	Active TSS	Ovary	ovary
29	chr3:46600000-46600600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:46600000-46600600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:46600000-46600600	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:46600000-46600600	Flanking Active TSS	Hela-S3	cervix
33	chr3:46600000-46600600	Active TSS	HepG2	liver
34	chr3:46600000-46600600	Flanking Active TSS	HSMM	muscle
35	chr3:46600000-46600600	Flanking Active TSS	HUVEC	blood vessel
36	chr3:46600000-46601000	Flanking Active TSS	Liver	Liver
37	chr3:46600200-46600600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:46600200-46600600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:46600200-46600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:46600200-46600600	Active TSS	Right Atrium	heart
41	chr3:46600200-46600600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:46600200-46600800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:46600200-46600800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:46600200-46601800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:46600200-46602200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:46600200-46602600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:46600200-46603000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:46600400-46600600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:46600400-46600600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:46600400-46600600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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