Variant report

Variant	rs1572603
Chromosome Location	chr1:47272403-47272404
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	MAX	chr1:47272371-47272827	MCF-7	breast:	n/a	chr1:47272599-47272615
2	STAT3	chr1:47272071-47272853	MCF10A-Er-Src	breast:	n/a	chr1:47272568-47272576
3	EP300	chr1:47272353-47272699	T-47D	breast:	n/a	chr1:47272662-47272678 chr1:47272459-47272473
4	FOS	chr1:47272232-47272741	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:47272232-47272721	MCF10A-Er-Src	breast:	n/a	chr1:47272568-47272576
6	NR3C1	chr1:47272265-47272715	ECC-1	luminal epithelium:	n/a	chr1:47272505-47272519
7	CEBPB	chr1:47272347-47272776	ECC-1	luminal epithelium:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
8	FOS	chr1:47272199-47272662	MCF10A-Er-Src	breast:	n/a	n/a
9	USF1	chr1:47272389-47272833	ECC-1	luminal epithelium:	n/a	chr1:47272595-47272606
10	ELF1	chr1:47272335-47272757	MCF-7	breast:	n/a	chr1:47272463-47272474
11	NR3C1	chr1:47272372-47272667	A549	lung:	n/a	chr1:47272505-47272519
12	CEBPB	chr1:47272373-47272770	ECC-1	luminal epithelium:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
13	CTCF	chr1:47272400-47272550	NHEK	skin:	n/a	n/a
14	FOS	chr1:47272313-47272600	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:47272080-47272441	MCF10A-Er-Src	breast:	n/a	n/a
16	NR3C1	chr1:47272285-47272726	A549	lung:	n/a	chr1:47272505-47272519
17	MYC	chr1:47271876-47272877	MCF10A-Er-Src	breast:	n/a	chr1:47272599-47272615
18	CEBPB	chr1:47272175-47272836	MCF-7	breast:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
19	NR3C1	chr1:47272334-47272757	A549	lung:	n/a	chr1:47272505-47272519 chr1:47272727-47272741
20	REST	chr1:47272335-47272833	MCF-7	breast:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
21	GATA3	chr1:47272274-47272887	MCF-7	breast:	n/a	chr1:47272461-47272471
22	FOS	chr1:47272171-47272710	MCF10A-Er-Src	breast:	n/a	chr1:47272180-47272187
23	NR3C1	chr1:47272380-47272652	A549	lung:	n/a	chr1:47272505-47272519
24	CEBPB	chr1:47272398-47272736	Hela-S3	cervix:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
25	POLR2A	chr1:47271497-47272686	MCF10A-Er-Src	breast:	n/a	n/a
26	STAT3	chr1:47272110-47272702	MCF10A-Er-Src	breast:	n/a	chr1:47272568-47272576
27	REST	chr1:47272389-47272847	ECC-1	luminal epithelium:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
28	USF1	chr1:47272357-47272718	ECC-1	luminal epithelium:	n/a	chr1:47272595-47272606
29	MYC	chr1:47272238-47272688	MCF10A-Er-Src	breast:	n/a	chr1:47272599-47272615
30	STAT3	chr1:47272285-47272737	MCF10A-Er-Src	breast:	n/a	chr1:47272568-47272576
31	GATA3	chr1:47272200-47272701	T-47D	breast:	n/a	chr1:47272461-47272471
32	REST	chr1:47272401-47272786	PFSK-1	brain:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
33	NR3C1	chr1:47272376-47272628	A549	lung:	n/a	chr1:47272505-47272519
34	CEBPB	chr1:47272292-47272727	HepG2	liver:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
35	NR3C1	chr1:47272280-47272767	A549	lung:	n/a	chr1:47272505-47272519 chr1:47272727-47272741
36	NR3C1	chr1:47272313-47272689	ECC-1	luminal epithelium:	n/a	chr1:47272505-47272519

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47272192..47274421-chr1:47282299..47283950,2	K562	blood:
2	chr1:47263957..47267463-chr1:47271063..47272982,3	MCF-7	breast:

Variant related genes	Relation type
CYP4B1	TF binding region
ENSG00000142973	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11211366	0.85[ASN][1000 genomes]
rs11211369	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211387	0.81[EUR][1000 genomes]
rs1122582	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11576162	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11583378	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11584320	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11586184	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12402717	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12410657	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566735	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12569216	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12758424	0.82[EUR][1000 genomes]
rs1890246	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1890248	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1890249	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1890250	1.00[ASN][1000 genomes]
rs1890251	1.00[ASN][1000 genomes]
rs2185032	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2405335	0.87[ASN][1000 genomes]
rs34560486	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3766195	0.87[ASN][1000 genomes]
rs3766196	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766197	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3820080	0.89[ASN][1000 genomes]
rs4417002	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45563134	0.85[ASN][1000 genomes]
rs4560983	0.90[EUR][1000 genomes]
rs4646482	0.87[ASN][1000 genomes]
rs4646486	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646487	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4646492	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646493	0.86[ASN][1000 genomes]
rs4646495	0.87[ASN][1000 genomes]
rs4660960	0.90[EUR][1000 genomes]
rs55868139	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55936777	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60430993	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67678353	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72637963	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72681939	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs751027	0.88[ASN][1000 genomes]
rs7553652	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs837395	0.88[ASN][1000 genomes]
rs9728536	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv546165	chr1:47266590-47272785	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1004143	chr1:47270942-47321982	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr1:47265600-47279200	Weak transcription	Gastric	stomach
2	chr1:47266400-47273800	Enhancers	Placenta	Placenta
3	chr1:47267800-47273000	Enhancers	Esophagus	oesophagus
4	chr1:47267800-47273600	Enhancers	Lung	lung
5	chr1:47268400-47273600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:47269800-47273600	Enhancers	Left Ventricle	heart
7	chr1:47270600-47273600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:47271200-47273000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:47271200-47273000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr1:47271200-47273200	Weak transcription	Right Ventricle	heart
11	chr1:47271400-47273600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:47271400-47273800	Enhancers	Fetal Intestine Small	intestine
13	chr1:47271600-47273000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:47271600-47273800	Enhancers	Fetal Intestine Large	intestine
15	chr1:47271800-47273400	Enhancers	Spleen	Spleen
16	chr1:47271800-47273600	Enhancers	Fetal Muscle Leg	muscle
17	chr1:47272000-47273200	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:47272000-47273400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:47272200-47272800	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:47272200-47273000	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:47272200-47273600	Enhancers	Right Atrium	heart
22	chr1:47272400-47272600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:47272400-47272800	Enhancers	Adipose Nuclei	Adipose
24	chr1:47272400-47273000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:47272400-47273000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:47272400-47273800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:47272400-47275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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