Variant report

Variant	rs3806702
Chromosome Location	chr3:46617502-46617503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr3:46615316-46617659	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr3:46617106-46617610	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF12	chr3:46617385-46617590	H1-hESC	embryonic stem cell:	n/a	chr3:46617547-46617557
4	POLR2A	chr3:46616859-46617721	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr3:46616839-46617732	H1-hESC	embryonic stem cell:	n/a	chr3:46616896-46616905
6	ATF2	chr3:46615333-46617713	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:46617088-46617734	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr3:46615328-46617611	H1-hESC	embryonic stem cell:	n/a	chr3:46617317-46617331 chr3:46617401-46617410
9	CHD1	chr3:46615351-46617726	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:46617264-46617687	H1-hESC	embryonic stem cell:	n/a	n/a
11	GTF2F1	chr3:46616878-46617552	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr3:46616748-46617641	H1-hESC	embryonic stem cell:	n/a	chr3:46616896-46616905
13	TEAD4	chr3:46616902-46617770	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:46616366-46619569	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr3:46615156-46617623	H1-hESC	embryonic stem cell:	n/a	chr3:46616912-46616926
16	TBP	chr3:46615704-46617729	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr3:46617263-46617687	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:46617366-46617512	MCF10A-Er-Src	breast:	n/a	n/a
19	CTBP2	chr3:46616463-46617666	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr3:46617158-46617736	H1-hESC	embryonic stem cell:	n/a	n/a
21	BACH1	chr3:46616742-46617607	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:46615452-46619820	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF7	chr3:46615582-46617740	H1-hESC	embryonic stem cell:	n/a	n/a
24	NANOG	chr3:46617298-46617713	H1-hESC	embryonic stem cell:	n/a	n/a

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:

Variant related genes	Relation type
TDGF1	TF binding region
ENSG00000241186	Chromatin interaction
ENSG00000163827	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1049667	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs11705987	1.00[MEX][hapmap]
rs11718490	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12185926	0.98[ASN][1000 genomes]
rs12637699	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13096172	0.98[ASN][1000 genomes]
rs13098842	0.85[EUR][1000 genomes]
rs17220622	1.00[MEX][hapmap]
rs2001441	0.98[ASN][1000 genomes]
rs3806701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806703	0.94[ASN][1000 genomes]
rs6442006	0.85[EUR][1000 genomes]
rs6769392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs7650998	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs939408	0.97[ASN][1000 genomes]
rs9682509	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3806702	TDGF1	cis	Muscle Skeletal	GTEx
rs3806702	LRRC2	cis	cerebellum	SCAN
rs3806702	FYCO1	cis	parietal	SCAN
rs3806702	ALS2CL	cis	cerebellum	SCAN
rs3806702	TDGF1	cis	cerebellum	SCAN
rs3806702	TDGF1	cis	parietal	SCAN
rs3806702	TDGF1	cis	Adipose Subcutaneous	GTEx
rs3806702	ABHD5	cis	parietal	SCAN
rs3806702	CDCP1	cis	cerebellum	SCAN
rs3806702	TDGF1	cis	Nerve Tibial	GTEx
rs3806702	TDGF1	cis	Esophagus Muscularis	GTEx
rs3806702	TDGF1///TDGF3	cis	normal skin	skin_eQTL
rs3806702	MAP4	cis	parietal	SCAN
rs3806702	TDGF1	cis	Heart Left Ventricle	GTEx
rs3806702	SLC38A3	cis	cerebellum	SCAN
rs3806702	TDGF1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46614400-46617800	Enhancers	HepG2	liver
3	chr3:46615200-46617600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:46615200-46617600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:46615200-46618400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:46615200-46618800	Enhancers	Fetal Heart	heart
7	chr3:46615200-46620400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:46615400-46619400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:46615800-46617600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:46615800-46617600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:46615800-46617600	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr3:46615800-46618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:46616200-46617600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:46616200-46620400	Weak transcription	Stomach Mucosa	stomach
15	chr3:46616400-46617600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:46616400-46617800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:46616400-46617800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr3:46616600-46618200	Weak transcription	Left Ventricle	heart
19	chr3:46616600-46618200	Weak transcription	Spleen	Spleen
20	chr3:46616600-46618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:46616600-46620600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:46616800-46620800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
24	chr3:46617000-46620600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:46617200-46617600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:46617200-46620600	Weak transcription	Liver	Liver
27	chr3:46617200-46621600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr3:46617400-46617600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:46617400-46617600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr3:46617400-46617600	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr3:46617400-46617600	Weak transcription	Lung	lung
32	chr3:46617400-46617800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:46617400-46618000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:46617400-46620400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:46617400-46620800	Weak transcription	Gastric	stomach

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