Variant report

Variant	rs3806703
Chromosome Location	chr3:46618501-46618502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr3:46617971-46619896	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr3:46618436-46618785	H1-hESC	embryonic stem cell:	n/a	chr3:46618669-46618677
3	RAD21	chr3:46618383-46618856	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr3:46618439-46618899	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr3:46618464-46618701	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:46618296-46618866	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr3:46618406-46619419	H1-hESC	embryonic stem cell:	n/a	n/a
8	BACH1	chr3:46618330-46618732	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3AK20	chr3:46618433-46618827	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr3:46618451-46618888	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:46618217-46618935	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:46616366-46619569	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr3:46618345-46618803	H1-hESC	embryonic stem cell:	n/a	chr3:46618669-46618677
14	TAF7	chr3:46617846-46619988	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr3:46618214-46618830	H1-hESC	embryonic stem cell:	n/a	chr3:46618629-46618639
16	POLR2A	chr3:46617965-46618868	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr3:46618280-46619708	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD2	chr3:46618492-46618840	H1-hESC	embryonic stem cell:	n/a	n/a
19	GTF2F1	chr3:46618331-46618806	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr3:46618488-46618894	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD1	chr3:46617928-46621284	H1-hESC	embryonic stem cell:	n/a	chr3:46619179-46619189
22	POLR2A	chr3:46615452-46619820	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46615629..46619191-chr3:46619379..46621638,3	K562	blood:
2	chr3:46616725..46618577-chr3:46625163..46627134,2	K562	blood:

No data

Variant related genes	Relation type
TDGF1	TF binding region
ENSG00000241186	Chromatin interaction
ENSG00000163827	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	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12185926	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13096172	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806701	0.96[ASN][1000 genomes]
rs3806702	0.94[ASN][1000 genomes]
rs6769392	0.96[ASN][1000 genomes]
rs6783573	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650998	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs939408	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9682509	0.96[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
rs3806703	TDGF1	cis	Heart Left Ventricle	GTEx
rs3806703	TDGF1	cis	Nerve Tibial	GTEx
rs3806703	TDGF1	cis	lung	GTEx
rs3806703	TDGF1	cis	Esophagus Muscularis	GTEx
rs3806703	TDGF1	cis	Muscle Skeletal	GTEx
rs3806703	TDGF1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46615200-46618800	Enhancers	Fetal Heart	heart
3	chr3:46615200-46620400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:46615400-46619400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:46615800-46618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:46616200-46620400	Weak transcription	Stomach Mucosa	stomach
7	chr3:46616600-46620600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:46616800-46620800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
10	chr3:46617000-46620600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:46617200-46620600	Weak transcription	Liver	Liver
12	chr3:46617200-46621600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr3:46617400-46620400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:46617400-46620800	Weak transcription	Gastric	stomach
15	chr3:46617600-46618600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:46617600-46620600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:46617600-46620800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:46617800-46619400	Weak transcription	HepG2	liver
19	chr3:46618000-46618800	Bivalent Enhancer	Fetal Lung	lung
20	chr3:46618200-46618600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
21	chr3:46618200-46618600	Enhancers	Left Ventricle	heart
22	chr3:46618200-46618600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
23	chr3:46618200-46618600	Enhancers	Spleen	Spleen
24	chr3:46618200-46618800	Bivalent Enhancer	Primary B cells from cord blood	blood
25	chr3:46618200-46618800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:46618200-46618800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr3:46618200-46618800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
28	chr3:46618200-46619200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr3:46618200-46620400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr3:46618200-46620600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:46618200-46620800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:46618200-46622200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:46618400-46618600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:46618400-46618600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr3:46618400-46618600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr3:46618400-46618600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:46618400-46618600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:46618400-46618600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:46618400-46618600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:46618400-46618600	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr3:46618400-46618600	Bivalent Enhancer	Brain Hippocampus Middle	brain
42	chr3:46618400-46618600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
43	chr3:46618400-46618600	Bivalent Enhancer	Fetal Brain Female	brain
44	chr3:46618400-46618600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr3:46618400-46618600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
46	chr3:46618400-46618600	Enhancers	Lung	lung
47	chr3:46618400-46618800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:46618400-46618800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr3:46618400-46618800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:46618400-46618800	Active TSS	Ovary	ovary

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