Variant report

Variant	rs1547949
Chromosome Location	chr3:53568580-53568581
allele	A/G
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	GATA3	chr3:53568171-53568598	SK-N-SH	brain:	n/a	chr3:53568359-53568375 chr3:53568363-53568370 chr3:53568363-53568370 chr3:53568363-53568370
2	EP300	chr3:53568236-53568585	SK-N-SH_RA	brain:	n/a	chr3:53568506-53568522
3	EP300	chr3:53567379-53571150	SK-N-SH	brain:	n/a	chr3:53568506-53568522 chr3:53569655-53569665 chr3:53569443-53569457 chr3:53570224-53570233
4	GATA3	chr3:53568179-53568624	SK-N-SH	brain:	n/a	chr3:53568359-53568375 chr3:53568363-53568370 chr3:53568363-53568370 chr3:53568363-53568370
5	REST	chr3:53568303-53568674	SK-N-SH	brain:	n/a	chr3:53568599-53568612
6	GATA2	chr3:53568181-53568637	SH-SY5Y	brain:	n/a	chr3:53568359-53568375 chr3:53568363-53568370 chr3:53568363-53568370 chr3:53568363-53568370

Variant related genes	Relation type
ENSG00000251987	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1074235	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1547951	0.93[EUR][1000 genomes]
rs17788662	0.86[CHB][hapmap]
rs33999362	0.84[ASN][1000 genomes]
rs3774424	0.85[CHB][hapmap]
rs3774428	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs3774440	0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs3821846	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs3821847	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs55828852	0.91[EUR][1000 genomes]
rs59422128	0.94[ASN][1000 genomes]
rs59512909	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62251864	0.91[ASN][1000 genomes]
rs62251868	0.90[ASN][1000 genomes]
rs62251869	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62251870	0.87[ASN][1000 genomes]
rs62251903	0.87[ASN][1000 genomes]
rs62251904	0.87[ASN][1000 genomes]
rs62251905	0.86[EUR][1000 genomes]
rs6764908	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs72957281	0.93[ASN][1000 genomes]
rs740756	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes];0.91[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53560600-53587000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53561000-53568800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:53563600-53569400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:53564800-53568600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:53564800-53579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53566400-53569000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:53566400-53569600	Strong transcription	Fetal Intestine Large	intestine
8	chr3:53566400-53583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:53566800-53569000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:53566800-53569200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:53566800-53569200	Strong transcription	Fetal Intestine Small	intestine
12	chr3:53566800-53570600	Enhancers	Fetal Lung	lung
13	chr3:53567200-53569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:53567800-53569000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:53567800-53569600	Enhancers	Fetal Brain Male	brain
16	chr3:53567800-53569800	Enhancers	Fetal Kidney	kidney
17	chr3:53567800-53579400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:53568200-53568600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:53568400-53568600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr3:53568400-53568600	Enhancers	Pancreas	Pancrea
21	chr3:53568400-53568800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:53568400-53569600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:53568400-53570200	Enhancers	Fetal Brain Female	brain

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