Variant report

Variant	rs59422128
Chromosome Location	chr3:53569303-53569304
allele	A/C
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	EP300	chr3:53567379-53571150	SK-N-SH	brain:	n/a	chr3:53568506-53568522 chr3:53569655-53569665 chr3:53569443-53569457 chr3:53570224-53570233
2	KAP1	chr3:53569024-53569542	HEK293	kidney:	n/a	chr3:53569106-53569114
3	REST	chr3:53569047-53569444	SK-N-SH	brain:	n/a	n/a
4	TCF7L2	chr3:53569225-53570109	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000251987	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1074235	0.93[ASN][1000 genomes]
rs1547949	0.94[ASN][1000 genomes]
rs17053168	0.92[EUR][1000 genomes]
rs33999362	0.86[ASN][1000 genomes]
rs3774428	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774439	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3774440	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774441	0.92[EUR][1000 genomes]
rs3821847	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59512909	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62251864	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251868	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251869	0.93[ASN][1000 genomes]
rs62251870	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251903	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251904	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6764908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72957281	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740756	0.97[ASN][1000 genomes]
rs9311502	0.90[EUR][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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53560600-53587000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53563600-53569400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53564800-53579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53566400-53569600	Strong transcription	Fetal Intestine Large	intestine
5	chr3:53566400-53583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:53566800-53570600	Enhancers	Fetal Lung	lung
7	chr3:53567800-53569600	Enhancers	Fetal Brain Male	brain
8	chr3:53567800-53569800	Enhancers	Fetal Kidney	kidney
9	chr3:53567800-53579400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53568400-53569600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:53568400-53570200	Enhancers	Fetal Brain Female	brain
12	chr3:53568600-53569400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:53568800-53569400	Bivalent Enhancer	Fetal Stomach	stomach
14	chr3:53568800-53569800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:53569000-53569400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr3:53569000-53569400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:53569000-53569400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:53569000-53569400	Enhancers	Pancreas	Pancrea
19	chr3:53569000-53569600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:53569000-53569800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:53569200-53569400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:53569200-53569400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:53569200-53569400	Genic enhancers	Fetal Intestine Small	intestine
24	chr3:53569200-53569400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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