Variant report

Variant	rs56009835
Chromosome Location	chr3:43078412-43078413
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	TBP	chr3:43078387-43078600	GM12878	blood:	n/a	n/a
2	BHLHE40	chr3:43078382-43078582	GM12878	blood:	n/a	n/a
3	RCOR1	chr3:43078388-43078523	GM12878	blood:	n/a	n/a
4	CHD2	chr3:43078405-43078594	GM12878	blood:	n/a	n/a
5	EP300	chr3:43078331-43078669	GM12878	blood:	n/a	n/a
6	CEBPB	chr3:43078407-43078780	K562	blood:	n/a	chr3:43078583-43078594
7	CEBPB	chr3:43078406-43078774	HepG2	liver:	n/a	chr3:43078583-43078594
8	CEBPB	chr3:43078410-43078698	K562	blood:	n/a	chr3:43078583-43078594
9	RUNX3	chr3:43078259-43078621	GM12878	blood:	n/a	n/a
10	EP300	chr3:43078352-43078653	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000232375	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13061038	0.86[ASN][1000 genomes]
rs13095711	0.99[ASN][1000 genomes]
rs2280565	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936817	0.95[ASN][1000 genomes]
rs34970115	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35339908	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs473467	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs477594	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs496436	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504973	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536119	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs606336	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62247065	0.80[ASN][1000 genomes]
rs643663	0.95[ASN][1000 genomes]
rs648273	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658958	0.95[ASN][1000 genomes]
rs660446	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806706	0.80[ASN][1000 genomes]
rs697327	0.93[ASN][1000 genomes]
rs870238	0.90[ASN][1000 genomes]
rs9311333	0.84[ASN][1000 genomes]
rs9882262	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
2	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:43067600-43084000	Weak transcription	Aorta	Aorta
6	chr3:43070600-43084800	Weak transcription	Esophagus	oesophagus
7	chr3:43073400-43084600	Weak transcription	Brain Angular Gyrus	brain
8	chr3:43073400-43084600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:43073600-43084400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:43074600-43084200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:43074800-43081200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:43075200-43084200	Weak transcription	Ovary	ovary
13	chr3:43076200-43078800	Strong transcription	Fetal Stomach	stomach
14	chr3:43076200-43079000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:43076600-43078800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:43076600-43079000	Enhancers	Fetal Muscle Leg	muscle
17	chr3:43076800-43079000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:43077200-43084400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:43077600-43084600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:43077800-43078600	Enhancers	Brain Substantia Nigra	brain
21	chr3:43077800-43080000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr3:43078000-43079200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:43078200-43078800	Strong transcription	Liver	Liver
24	chr3:43078400-43084200	Weak transcription	Placenta	Placenta

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