Variant report

Variant	rs72974339
Chromosome Location	chr3:133461739-133461740
allele	A/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	NR3C1	chr3:133461229-133461859	A549	lung:	n/a	n/a
2	MAX	chr3:133461673-133461749	NB4	blood:	n/a	n/a
3	MYBL2	chr3:133461041-133462143	HepG2	liver:	n/a	n/a
4	FOXA1	chr3:133461244-133462392	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
5	MXI1	chr3:133461345-133461923	HepG2	liver:	n/a	n/a
6	EP300	chr3:133461232-133462003	MCF-7	breast:	n/a	chr3:133461585-133461595
7	REST	chr3:133461361-133461829	HepG2	liver:	n/a	n/a
8	FOXA1	chr3:133461222-133462197	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
9	FOXA1	chr3:133461271-133462507	HepG2	liver:	n/a	chr3:133461580-133461595 chr3:133461892-133461904 chr3:133461582-133461594
10	NR2F2	chr3:133461210-133462378	MCF-7	breast:	n/a	n/a
11	NR3C1	chr3:133461323-133461841	A549	lung:	n/a	n/a
12	SP1	chr3:133461213-133461860	A549	lung:	n/a	chr3:133461397-133461411
13	MYBL2	chr3:133460921-133462177	HepG2	liver:	n/a	n/a
14	EP300	chr3:133461387-133461824	SK-N-SH_RA	brain:	n/a	chr3:133461585-133461595
15	MBD4	chr3:133461277-133462081	HepG2	liver:	n/a	n/a
16	BHLHE40	chr3:133461227-133461823	HepG2	liver:	n/a	n/a
17	EP300	chr3:133461179-133461976	A549	lung:	n/a	chr3:133461585-133461595
18	RCOR1	chr3:133461426-133462454	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr3:133461418-133461749	HepG2	liver:	n/a	n/a
20	CTCF	chr3:133461600-133461750	HBMEC	blood vessel:	n/a	chr3:133461663-133461676
21	RCOR1	chr3:133461698-133462052	K562	blood:	n/a	n/a
22	FOXA1	chr3:133461397-133461827	T-47D	breast:	n/a	chr3:133461580-133461595 chr3:133461582-133461594
23	BRCA1	chr3:133461452-133461765	HepG2	liver:	n/a	n/a
24	EP300	chr3:133461251-133462049	HepG2	liver:	n/a	chr3:133461585-133461595
25	NFIC	chr3:133461118-133462076	HepG2	liver:	n/a	n/a
26	FOXM1	chr3:133461248-133461927	MCF-7	breast:	n/a	n/a
27	IRF1	chr3:133461722-133461952	K562	blood:	n/a	n/a
28	HNF4A	chr3:133461322-133461862	HepG2	liver:	n/a	n/a
29	HNF4A	chr3:133461372-133461828	HepG2	liver:	n/a	n/a
30	MAFF	chr3:133461390-133461831	HepG2	liver:	n/a	n/a
31	HEY1	chr3:133461180-133461991	HepG2	liver:	n/a	n/a
32	CTCF	chr3:133461660-133461810	HAc	cerebellar:	n/a	chr3:133461663-133461676
33	HDAC2	chr3:133461144-133462122	MCF-7	breast:	n/a	chr3:133461585-133461594
34	SRF	chr3:133461477-133461763	HepG2	liver:	n/a	n/a
35	MAFK	chr3:133461348-133461993	HepG2	liver:	n/a	n/a
36	MAX	chr3:133461364-133461871	HepG2	liver:	n/a	n/a
37	GATA3	chr3:133461084-133462420	MCF-7	breast:	n/a	chr3:133462043-133462050 chr3:133462043-133462050 chr3:133462043-133462050
38	EP300	chr3:133461170-133461934	A549	lung:	n/a	chr3:133461585-133461595
39	CTCF	chr3:133461600-133461750	HepG2	liver:	n/a	chr3:133461663-133461676
40	MAX	chr3:133461176-133462034	HepG2	liver:	n/a	n/a
41	ARID3A	chr3:133461243-133462145	HepG2	liver:	n/a	n/a
42	CTCF	chr3:133461620-133461770	Caco-2	colon:	n/a	chr3:133461663-133461676
43	RUNX3	chr3:133461589-133461883	GM12878	blood:	n/a	n/a
44	RXRA	chr3:133461266-133461972	HepG2	liver:	n/a	n/a
45	EP300	chr3:133461285-133461976	HepG2	liver:	n/a	chr3:133461585-133461595
46	FOXA2	chr3:133461267-133462102	A549	lung:	n/a	chr3:133461892-133461904 chr3:133461582-133461594
47	MAX	chr3:133461136-133462444	MCF-7	breast:	n/a	n/a
48	SIN3AK20	chr3:133461500-133461774	HepG2	liver:	n/a	n/a
49	CEBPB	chr3:133461302-133461811	HepG2	liver:	n/a	n/a
50	SP1	chr3:133461239-133462033	HepG2	liver:	n/a	chr3:133461397-133461411

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:133461738-133461788	GM12891	blood:	n/a
2	chr3:133461738-133461788	GM06990	blood:	n/a
3	chr3:133461738-133461788	AoSMC	blood vessel:	n/a
4	chr3:133461738-133461788	GM12878	blood:	n/a
5	chr3:133461738-133461788	H1-hESC	embryonic stem cell:	embryo
6	chr3:133461738-133461788	AG09319	gingival:	n/a
7	chr3:133461738-133461788	ProgFib	skin:	n/a
8	chr3:133461738-133461788	BE2_C	brain:	n/a
9	chr3:133461738-133461788	Caco-2	colon:	n/a
10	chr3:133461738-133461788	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:133461738-133461788	A549	lung:	n/a
12	chr3:133461738-133461788	LNCaP	prostate:	n/a
13	chr3:133461738-133461788	HRPEpiC	eye:	n/a
14	chr3:133461738-133461788	NT2-D1	testis:	n/a
15	chr3:133461738-133461788	HRE	kidney:	n/a
16	chr3:133461738-133461788	AG04449	skin:	fetal
17	chr3:133461738-133461788	AG09309	skin:	n/a
18	chr3:133461738-133461788	AG04450	lung:	fetal
19	chr3:133461738-133461788	GM12892	blood:	n/a
20	chr3:133461738-133461788	ovcar-3	ovarian:	n/a
21	chr3:133461738-133461788	HAEpiC	amniotic membrane:	n/a
22	chr3:133461738-133461788	SKMC	muscle:	n/a
23	chr3:133461738-133461788	HMEC	breast:	n/a
24	chr3:133461738-133461788	SK-N-SH_RA	brain:	n/a
25	chr3:133461738-133461788	HEK293	kidney:	embryo
26	chr3:133461738-133461788	Hepatocyte	liver:	n/a
27	chr3:133461738-133461788	HRCEpiC	kidney:	n/a
28	chr3:133461738-133461788	Hela-S3	cervix:	n/a
29	chr3:133461738-133461788	PANC-1	pancreas:	n/a
30	chr3:133461738-133461788	HCF	heart:	n/a
31	chr3:133461738-133461788	AG10803	skin:	n/a
32	chr3:133461738-133461788	K562	blood:	n/a
33	chr3:133461738-133461788	HL-60	blood:	n/a
34	chr3:133461738-133461788	NHBE	bronchial:	n/a
35	chr3:133461738-133461788	ECC-1	luminal epithelium:	n/a
36	chr3:133461738-133461788	BJ	skin:	n/a
37	chr3:133461738-133461788	U87	brain:	n/a
38	chr3:133461738-133461788	Jurkat	blood:	n/a
39	chr3:133461738-133461788	HCM	heart:	n/a
40	chr3:133461738-133461788	GM19239	blood:	n/a
41	chr3:133461738-133461788	NHDF-neo	bronchial:	n/a
42	chr3:133461738-133461788	HUVEC	blood vessel:	n/a
43	chr3:133461738-133461788	SK-N-MC	brain:	n/a
44	chr3:133461738-133461788	MCF10A-Er-Src	breast:	n/a
45	chr3:133461738-133461788	MCF-7	breast:	n/a
46	chr3:133461738-133461788	HNPCEpiC	eye:	n/a
47	chr3:133461738-133461788	NB4	blood:	n/a
48	chr3:133461738-133461788	RPTEC	kidney:	n/a
49	chr3:133461738-133461788	PFSK-1	brain:	n/a
50	chr3:133461738-133461788	HCPEpiC	choroid plexus:	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
TF	CpG island
ENSG00000242337	Chromatin interaction
ENSG00000091513	Chromatin interaction
ENSG00000163781	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs59353183	1.00[AFR][1000 genomes]
rs60088317	1.00[AFR][1000 genomes]
rs72972297	1.00[AFR][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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133460400-133464600	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr3:133460800-133462200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:133460800-133462600	Flanking Active TSS	Liver	Liver
4	chr3:133460800-133462800	Enhancers	Pancreas	Pancrea
5	chr3:133460800-133464600	Enhancers	Brain Angular Gyrus	brain
6	chr3:133461000-133462000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:133461200-133461800	Active TSS	A549	lung
8	chr3:133461200-133462000	Enhancers	Fetal Lung	lung
9	chr3:133461200-133462000	Bivalent Enhancer	Osteobl	bone
10	chr3:133461200-133462400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:133461400-133461800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
12	chr3:133461400-133461800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:133461400-133461800	Active TSS	HepG2	liver
14	chr3:133461400-133461800	Flanking Bivalent TSS/Enh	HSMM	muscle
15	chr3:133461400-133462000	Enhancers	Fetal Kidney	kidney
16	chr3:133461400-133462200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:133461400-133462200	Enhancers	K562	blood
18	chr3:133461400-133462400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:133461400-133462400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:133461600-133461800	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr3:133461600-133461800	Enhancers	HSMMtube	muscle
22	chr3:133461600-133462000	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:133461600-133462000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:133461600-133462200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr3:133461600-133462400	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr3:133461600-133464400	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:133461600-133464400	Enhancers	Brain Substantia Nigra	brain

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