Variant report

Variant	rs2001441
Chromosome Location	chr3:46604376-46604377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46603881..46605418-chr3:46615085..46618078,2	K562	blood:

Variant related genes	Relation type
ENSG00000241186	Chromatin interaction

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

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

rs_ID	r²[population]
rs1049667	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096172	0.87[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	0.98[ASN][1000 genomes]
rs3806703	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769392	1.00[ASN][1000 genomes]
rs6783573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650998	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs939408	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[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
rs2001441	TDGF1	cis	Heart Left Ventricle	GTEx
rs2001441	TDGF1	cis	Esophagus Muscularis	GTEx
rs2001441	TDGF1	cis	Muscle Skeletal	GTEx
rs2001441	TDGF1	cis	Adipose Subcutaneous	GTEx
rs2001441	TDGF1	cis	lung	GTEx
rs2001441	TDGF1	cis	Nerve Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46591800-46606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:46600400-46606600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:46600400-46607200	Weak transcription	Gastric	stomach
4	chr3:46600600-46606600	Weak transcription	Thymus	Thymus
5	chr3:46600600-46606800	Weak transcription	Ovary	ovary
6	chr3:46601000-46606400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:46601000-46606600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:46601200-46606000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:46601200-46607200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:46601600-46605600	Weak transcription	NHDF-Ad	bronchial
11	chr3:46601800-46605200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:46602000-46606000	Enhancers	Left Ventricle	heart
13	chr3:46602000-46607000	Weak transcription	Liver	Liver
14	chr3:46602400-46604800	Weak transcription	Esophagus	oesophagus
15	chr3:46602400-46606200	Weak transcription	Right Ventricle	heart
16	chr3:46602400-46607000	Weak transcription	Right Atrium	heart
17	chr3:46602600-46605400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:46602800-46604800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:46602800-46605200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:46602800-46606200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:46603200-46604600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr3:46603200-46605000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:46603400-46604600	Weak transcription	Psoas Muscle	Psoas
24	chr3:46603400-46604800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:46603400-46604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:46603400-46606400	Enhancers	Fetal Heart	heart
27	chr3:46603800-46604600	Weak transcription	Lung	lung
28	chr3:46604000-46604600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:46604000-46604800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:46604000-46606000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:46604000-46606600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:46604200-46604400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:46604200-46604400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:46604200-46605000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:46604200-46605600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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