Variant report

Variant	rs1890250
Chromosome Location	chr1:47272785-47272786
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	RAD21	chr1:47272744-47273031	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF1	chr1:47272389-47272833	ECC-1	luminal epithelium:	n/a	chr1:47272595-47272606
5	MYC	chr1:47271876-47272877	MCF10A-Er-Src	breast:	n/a	chr1:47272599-47272615
6	CEBPB	chr1:47272175-47272836	MCF-7	breast:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
7	REST	chr1:47272335-47272833	MCF-7	breast:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
8	GATA3	chr1:47272274-47272887	MCF-7	breast:	n/a	chr1:47272461-47272471
9	CEBPB	chr1:47272435-47272799	MCF-7	breast:	n/a	chr1:47272566-47272577 chr1:47272565-47272578
10	REST	chr1:47272389-47272847	ECC-1	luminal epithelium:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
11	REST	chr1:47272401-47272786	PFSK-1	brain:	n/a	chr1:47272582-47272591 chr1:47272672-47272681
12	REST	chr1:47272423-47272794	MCF-7	breast:	n/a	chr1:47272582-47272591 chr1:47272672-47272681

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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11211366	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211369	0.84[ASN][1000 genomes]
rs1122582	0.85[ASN][1000 genomes]
rs11576162	0.89[ASN][1000 genomes]
rs11583378	0.85[ASN][1000 genomes]
rs11586184	0.85[ASN][1000 genomes]
rs12402717	0.84[ASN][1000 genomes]
rs12410657	0.94[ASN][1000 genomes]
rs12569216	0.84[ASN][1000 genomes]
rs1572603	1.00[ASN][1000 genomes]
rs1890251	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185032	0.85[ASN][1000 genomes]
rs2405335	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766195	0.87[ASN][1000 genomes]
rs3766196	0.87[ASN][1000 genomes]
rs3766197	0.89[ASN][1000 genomes]
rs3820080	0.89[ASN][1000 genomes]
rs45563134	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4646482	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4646486	0.93[ASN][1000 genomes]
rs4646487	0.93[ASN][1000 genomes]
rs4646492	0.89[ASN][1000 genomes]
rs4646493	0.86[ASN][1000 genomes]
rs4646495	0.87[ASN][1000 genomes]
rs55868139	0.84[ASN][1000 genomes]
rs55936777	0.85[ASN][1000 genomes]
rs60430993	0.85[ASN][1000 genomes]
rs668770	0.94[EUR][1000 genomes]
rs67678353	0.85[ASN][1000 genomes]
rs681840	0.96[EUR][1000 genomes]
rs72637963	0.94[ASN][1000 genomes]
rs751027	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7553652	0.83[ASN][1000 genomes]
rs837395	0.96[EUR][1000 genomes];0.88[ASN][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:26 , 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	chr1:47272400-47272800	Enhancers	Adipose Nuclei	Adipose
23	chr1:47272400-47273000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:47272400-47273000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:47272400-47273800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:47272400-47275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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