Variant report

Variant	rs12633707
Chromosome Location	chr3:42773423-42773424
allele	C/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	EP300	chr3:42773296-42773435	HepG2	liver:	n/a	n/a
2	FOXA2	chr3:42773264-42774298	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
CCDC13-AS1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10490794	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865922	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11929390	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12054446	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12487729	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491179	0.92[ASN][1000 genomes]
rs12635736	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070345	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240859	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339684	0.92[ASN][1000 genomes]
rs339731	0.92[ASN][1000 genomes]
rs34549959	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3895740	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3907218	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3912104	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3916334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60706321	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6807878	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7639170	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639483	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830553	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839430	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42760400-42773600	Enhancers	Brain Substantia Nigra	brain
2	chr3:42763600-42773600	Enhancers	Brain Anterior Caudate	brain
3	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
4	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:42769000-42773600	Enhancers	Brain Hippocampus Middle	brain
7	chr3:42769000-42774200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:42769800-42774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:42769800-42787600	Weak transcription	Gastric	stomach
13	chr3:42770200-42774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:42771000-42774000	Enhancers	Right Ventricle	heart
16	chr3:42771000-42774200	Enhancers	Right Atrium	heart
17	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:42772200-42773800	Weak transcription	Psoas Muscle	Psoas
19	chr3:42772600-42773600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
21	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:42773000-42774600	Enhancers	Pancreas	Pancrea
23	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:42773200-42773600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:42773200-42774400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:42773400-42773600	Enhancers	Fetal Muscle Leg	muscle
28	chr3:42773400-42773800	Flanking Active TSS	HepG2	liver
29	chr3:42773400-42774400	Weak transcription	Fetal Heart	heart
30	chr3:42773400-42774600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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