Variant report

Variant	rs57865489
Chromosome Location	chr3:46615636-46615637
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	YY1	chr3:46615492-46616199	H1-hESC	embryonic stem cell:	n/a	chr3:46616006-46616017 chr3:46616009-46616018
2	CHD2	chr3:46615316-46617659	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr3:46615563-46616208	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr3:46615390-46616220	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr3:46615593-46616214	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:46615490-46616143	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr3:46615333-46617713	H1-hESC	embryonic stem cell:	n/a	n/a
8	HDAC2	chr3:46615566-46616169	H1-hESC	embryonic stem cell:	n/a	chr3:46615636-46615650
9	SIN3A	chr3:46615328-46617611	H1-hESC	embryonic stem cell:	n/a	chr3:46617317-46617331 chr3:46617401-46617410
10	CHD1	chr3:46615351-46617726	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr3:46615535-46616316	H1-hESC	embryonic stem cell:	n/a	chr3:46616008-46616018 chr3:46616007-46616019 chr3:46616008-46616017 chr3:46616009-46616018 chr3:46616007-46616019 chr3:46616008-46616022
12	NFIC	chr3:46615501-46616194	ECC-1	luminal epithelium:	n/a	n/a
13	ATF2	chr3:46615406-46616565	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF12	chr3:46615389-46616171	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr3:46615156-46617623	H1-hESC	embryonic stem cell:	n/a	chr3:46616912-46616926
16	TEAD4	chr3:46615417-46616164	ECC-1	luminal epithelium:	n/a	n/a
17	TEAD4	chr3:46615601-46616253	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:46615452-46619820	H1-hESC	embryonic stem cell:	n/a	n/a
19	EP300	chr3:46615382-46616275	ECC-1	luminal epithelium:	n/a	n/a
20	TAF7	chr3:46615582-46617740	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:

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1520491	0.89[ASN][1000 genomes]
rs17221605	0.89[ASN][1000 genomes]
rs17287344	0.89[ASN][1000 genomes]
rs3806705	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56383925	0.89[ASN][1000 genomes]
rs6768139	0.84[AFR][1000 genomes]
rs939414	0.89[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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608200-46616400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:46608400-46617200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
4	chr3:46613000-46616000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:46614400-46617800	Enhancers	HepG2	liver
6	chr3:46615000-46617200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:46615200-46615800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:46615200-46616000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:46615200-46616200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr3:46615200-46617000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:46615200-46617000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:46615200-46617200	Enhancers	Liver	Liver
13	chr3:46615200-46617400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:46615200-46617400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:46615200-46617600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:46615200-46617600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:46615200-46618400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:46615200-46618800	Enhancers	Fetal Heart	heart
19	chr3:46615200-46620400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:46615400-46615800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:46615400-46616000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:46615400-46616200	Enhancers	K562	blood
23	chr3:46615400-46616600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:46615400-46619400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:46615600-46615800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:46615600-46615800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:46615600-46615800	Enhancers	Fetal Intestine Large	intestine
28	chr3:46615600-46615800	Bivalent Enhancer	NH-A	brain
29	chr3:46615600-46616000	Bivalent Enhancer	Fetal Lung	lung
30	chr3:46615600-46616000	Enhancers	Fetal Muscle Leg	muscle
31	chr3:46615600-46616000	Weak transcription	Stomach Mucosa	stomach
32	chr3:46615600-46616600	Enhancers	Skeletal Muscle Male	skeletal muscle

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