Variant report

Variant	rs12491179
Chromosome Location	chr3:42773962-42773963
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	FOXA1	chr3:42773652-42774836	HepG2	liver:	n/a	n/a
2	HDAC2	chr3:42773635-42774174	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:42773626-42774271	HepG2	liver:	n/a	n/a
4	MAX	chr3:42773717-42774693	HepG2	liver:	n/a	n/a
5	HEY1	chr3:42773888-42774254	HepG2	liver:	n/a	n/a
6	TCF12	chr3:42773718-42774182	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:42773521-42774201	HepG2	liver:	n/a	n/a
8	HSF1	chr3:42773735-42774883	HepG2	liver:	n/a	chr3:42774093-42774108
9	NFIC	chr3:42773665-42774687	HepG2	liver:	n/a	n/a
10	HEY1	chr3:42773587-42774701	HepG2	liver:	n/a	n/a
11	CEBPD	chr3:42773583-42773965	HepG2	liver:	n/a	n/a
12	MBD4	chr3:42773865-42774791	HepG2	liver:	n/a	n/a
13	FOXA1	chr3:42773619-42774296	HepG2	liver:	n/a	n/a
14	RAD21	chr3:42773774-42774752	HepG2	liver:	n/a	chr3:42774542-42774555
15	MYBL2	chr3:42773551-42774741	HepG2	liver:	n/a	n/a
16	CTCF	chr3:42773949-42774001	HepG2	liver:	n/a	n/a
17	NFIC	chr3:42773652-42774795	HepG2	liver:	n/a	n/a
18	ARID3A	chr3:42773812-42774155	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:42773525-42774674	HepG2	liver:	n/a	n/a
20	EP300	chr3:42773573-42774254	HepG2	liver:	n/a	n/a
21	MBD4	chr3:42773786-42774390	HepG2	liver:	n/a	n/a
22	MYBL2	chr3:42773515-42774763	HepG2	liver:	n/a	n/a
23	MXI1	chr3:42773631-42774714	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:42773734-42774534	HepG2	liver:	n/a	n/a
25	RCOR1	chr3:42773677-42774726	HepG2	liver:	n/a	n/a
26	EP300	chr3:42773672-42774721	HepG2	liver:	n/a	n/a
27	HNF4G	chr3:42773713-42774174	HepG2	liver:	n/a	chr3:42773997-42774019 chr3:42773948-42773963 chr3:42773926-42773934 chr3:42773954-42773962
28	ZBTB7A	chr3:42773767-42774148	HepG2	liver:	n/a	n/a
29	RXRA	chr3:42773481-42774185	HepG2	liver:	n/a	n/a
30	CEBPB	chr3:42773764-42774515	HepG2	liver:	n/a	chr3:42774320-42774333 chr3:42774321-42774332
31	JUND	chr3:42773843-42774703	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:42773440-42774627	HepG2	liver:	n/a	n/a
33	CHD2	chr3:42773553-42774013	HepG2	liver:	n/a	n/a
34	HDAC2	chr3:42773608-42774258	HepG2	liver:	n/a	n/a
35	FOXA1	chr3:42773617-42774798	HepG2	liver:	n/a	n/a
36	SP1	chr3:42773639-42774631	HepG2	liver:	n/a	n/a
37	MAZ	chr3:42773570-42774624	HepG2	liver:	n/a	n/a
38	EP300	chr3:42773566-42774702	HepG2	liver:	n/a	n/a
39	HNF4A	chr3:42773716-42774049	HepG2	liver:	n/a	chr3:42773997-42774019 chr3:42773926-42773934 chr3:42773954-42773962
40	MYC	chr3:42773745-42774235	HepG2	liver:	n/a	n/a
41	ZBTB7A	chr3:42773760-42774081	HepG2	liver:	n/a	n/a
42	HNF4A	chr3:42773701-42774203	HepG2	liver:	n/a	chr3:42773926-42773934 chr3:42773997-42774019 chr3:42773954-42773962
43	FOXA2	chr3:42773662-42774187	HepG2	liver:	n/a	n/a
44	RXRA	chr3:42773610-42774168	HepG2	liver:	n/a	n/a
45	FOXA2	chr3:42773264-42774298	HepG2	liver:	n/a	n/a
46	RAD21	chr3:42773584-42774146	HepG2	liver:	n/a	n/a
47	MAX	chr3:42773480-42774900	HepG2	liver:	n/a	n/a
48	TBP	chr3:42773807-42774280	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
CCDC13-AS1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10490794	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10865922	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11129975	0.85[EUR][1000 genomes]
rs11129976	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11129977	0.83[EUR][1000 genomes]
rs11718476	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11922251	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11922832	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs11929390	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12054446	0.82[ASN][1000 genomes]
rs12487729	0.89[ASN][1000 genomes]
rs12633707	0.92[ASN][1000 genomes]
rs12635736	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12639142	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13070029	0.86[EUR][1000 genomes]
rs13070345	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13096498	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2240859	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2372110	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs339671	0.90[EUR][1000 genomes]
rs339684	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34549959	0.88[ASN][1000 genomes]
rs34868846	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35584330	0.90[EUR][1000 genomes]
rs3843369	0.92[EUR][1000 genomes]
rs3846063	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3895740	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3907218	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3912104	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3916334	0.89[ASN][1000 genomes]
rs4683332	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs4683335	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs60706321	0.82[ASN][1000 genomes]
rs6442067	0.90[EUR][1000 genomes]
rs6779561	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs6807878	0.85[ASN][1000 genomes]
rs7639170	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7639483	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7641046	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs9830553	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9839430	0.89[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
2	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain
3	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:42769000-42774200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:42769800-42774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:42769800-42787600	Weak transcription	Gastric	stomach
10	chr3:42770200-42774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:42771000-42774000	Enhancers	Right Ventricle	heart
13	chr3:42771000-42774200	Enhancers	Right Atrium	heart
14	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
16	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:42773000-42774600	Enhancers	Pancreas	Pancrea
18	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:42773200-42774400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:42773400-42774400	Weak transcription	Fetal Heart	heart
22	chr3:42773400-42774600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:42773600-42774600	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr3:42773600-42775200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:42773600-42775600	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr3:42773600-42776400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:42773800-42774000	Enhancers	Brain Substantia Nigra	brain
28	chr3:42773800-42774000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr3:42773800-42774000	Enhancers	HepG2	liver
30	chr3:42773800-42774600	Enhancers	Psoas Muscle	Psoas
31	chr3:42773800-42775400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:42773800-42775400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:42773800-42775600	Enhancers	Brain Germinal Matrix	brain
34	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle

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