Variant report

Variant	rs1800276
Chromosome Location	chr3:133461551-133461552
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	NR3C1	chr3:133461229-133461859	A549	lung:	n/a	n/a
2	MYBL2	chr3:133461041-133462143	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:133461244-133462392	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
4	MXI1	chr3:133461345-133461923	HepG2	liver:	n/a	n/a
5	EP300	chr3:133461232-133462003	MCF-7	breast:	n/a	chr3:133461585-133461595
6	REST	chr3:133461361-133461829	HepG2	liver:	n/a	n/a
7	FOXA1	chr3:133461222-133462197	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
8	FOXA1	chr3:133461271-133462507	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
9	NR2F2	chr3:133461210-133462378	MCF-7	breast:	n/a	n/a
10	NR3C1	chr3:133461323-133461841	A549	lung:	n/a	n/a
11	SP1	chr3:133461213-133461860	A549	lung:	n/a	chr3:133461397-133461411
12	MYBL2	chr3:133460921-133462177	HepG2	liver:	n/a	n/a
13	EP300	chr3:133461387-133461824	SK-N-SH_RA	brain:	n/a	chr3:133461585-133461595
14	MBD4	chr3:133461277-133462081	HepG2	liver:	n/a	n/a
15	BHLHE40	chr3:133461227-133461823	HepG2	liver:	n/a	n/a
16	EP300	chr3:133461179-133461976	A549	lung:	n/a	chr3:133461585-133461595
17	RCOR1	chr3:133461426-133462454	HepG2	liver:	n/a	n/a
18	SIN3AK20	chr3:133461418-133461749	HepG2	liver:	n/a	n/a
19	FOXA1	chr3:133461397-133461827	T-47D	breast:	n/a	chr3:133461580-133461595 chr3:133461582-133461594
20	NR3C1	chr3:133461408-133461731	A549	lung:	n/a	n/a
21	BRCA1	chr3:133461452-133461765	HepG2	liver:	n/a	n/a
22	EP300	chr3:133461251-133462049	HepG2	liver:	n/a	chr3:133461585-133461595
23	NFIC	chr3:133461118-133462076	HepG2	liver:	n/a	n/a
24	FOXM1	chr3:133461248-133461927	MCF-7	breast:	n/a	n/a
25	HNF4A	chr3:133461322-133461862	HepG2	liver:	n/a	n/a
26	HNF4A	chr3:133461372-133461828	HepG2	liver:	n/a	n/a
27	MAFF	chr3:133461390-133461831	HepG2	liver:	n/a	n/a
28	HEY1	chr3:133461180-133461991	HepG2	liver:	n/a	n/a
29	HDAC2	chr3:133461144-133462122	MCF-7	breast:	n/a	chr3:133461585-133461594
30	SRF	chr3:133461477-133461763	HepG2	liver:	n/a	n/a
31	MAFK	chr3:133461348-133461993	HepG2	liver:	n/a	n/a
32	MAX	chr3:133461364-133461871	HepG2	liver:	n/a	n/a
33	GATA3	chr3:133461084-133462420	MCF-7	breast:	n/a	chr3:133462043-133462050 chr3:133462043-133462050 chr3:133462043-133462050
34	EP300	chr3:133461170-133461934	A549	lung:	n/a	chr3:133461585-133461595
35	CTCF	chr3:133461540-133461690	AG09319	gingival:	n/a	chr3:133461663-133461676
36	MAX	chr3:133461176-133462034	HepG2	liver:	n/a	n/a
37	ARID3A	chr3:133461243-133462145	HepG2	liver:	n/a	n/a
38	RXRA	chr3:133461266-133461972	HepG2	liver:	n/a	n/a
39	EP300	chr3:133461285-133461976	HepG2	liver:	n/a	chr3:133461585-133461595
40	FOXA2	chr3:133461267-133462102	A549	lung:	n/a	chr3:133461892-133461904 chr3:133461582-133461594
41	MAX	chr3:133461136-133462444	MCF-7	breast:	n/a	n/a
42	SIN3AK20	chr3:133461500-133461774	HepG2	liver:	n/a	n/a
43	CEBPB	chr3:133461302-133461811	HepG2	liver:	n/a	n/a
44	SP1	chr3:133461239-133462033	HepG2	liver:	n/a	chr3:133461397-133461411
45	EP300	chr3:133461179-133462086	HepG2	liver:	n/a	chr3:133461585-133461595
46	ZNF384	chr3:133461527-133461677	K562	blood:	n/a	n/a
47	MBD4	chr3:133461304-133462105	HepG2	liver:	n/a	n/a
48	NR2F2	chr3:133461260-133461978	HepG2	liver:	n/a	n/a
49	HDAC2	chr3:133461078-133461914	HepG2	liver:	n/a	chr3:133461585-133461594
50	CHD2	chr3:133461351-133461760	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133379775..133382913-chr3:133460288..133462996,3	MCF-7	breast:
2	chr3:133460249..133463891-chr3:133464263..133466995,3	MCF-7	breast:

Variant related genes	Relation type
TF	TF binding region
ENSG00000091513	Chromatin interaction
ENSG00000163781	Chromatin interaction
ENSG00000242337	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12638146	0.92[ASN][1000 genomes]
rs1800277	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785596	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796795	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177220	0.81[ASN][1000 genomes]
rs8177313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177321	0.80[AMR][1000 genomes];0.81[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133460400-133464600	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr3:133460600-133461600	Enhancers	Brain Anterior Caudate	brain
3	chr3:133460800-133462200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:133460800-133462600	Flanking Active TSS	Liver	Liver
5	chr3:133460800-133462800	Enhancers	Pancreas	Pancrea
6	chr3:133460800-133464600	Enhancers	Brain Angular Gyrus	brain
7	chr3:133461000-133462000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:133461200-133461600	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr3:133461200-133461600	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr3:133461200-133461600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr3:133461200-133461600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr3:133461200-133461600	Flanking Active TSS	HSMMtube	muscle
13	chr3:133461200-133461800	Active TSS	A549	lung
14	chr3:133461200-133462000	Enhancers	Fetal Lung	lung
15	chr3:133461200-133462000	Bivalent Enhancer	Osteobl	bone
16	chr3:133461200-133462400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:133461400-133461600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:133461400-133461600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:133461400-133461600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:133461400-133461600	Enhancers	Brain Hippocampus Middle	brain
21	chr3:133461400-133461800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
22	chr3:133461400-133461800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:133461400-133461800	Active TSS	HepG2	liver
24	chr3:133461400-133461800	Flanking Bivalent TSS/Enh	HSMM	muscle
25	chr3:133461400-133462000	Enhancers	Fetal Kidney	kidney
26	chr3:133461400-133462200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:133461400-133462200	Enhancers	K562	blood
28	chr3:133461400-133462400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:133461400-133462400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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