Variant report

Variant	rs2769274
Chromosome Location	chr1:151324415-151324416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:151324392-151325119	ECC-1	luminal epithelium:	n/a	n/a
2	SRF	chr1:151324401-151325167	ECC-1	luminal epithelium:	n/a	chr1:151324849-151324867 chr1:151324849-151324863
3	NFIC	chr1:151324355-151325175	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr1:151324407-151324934	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr1:151324338-151325125	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151324405..151326399-chr1:151329640..151331142,2	MCF-7	breast:
2	chr1:151322277..151325094-chr1:151343511..151345931,3	MCF-7	breast:
3	chr1:151319634..151321435-chr1:151323050..151325074,3	K562	blood:
4	chr1:151323025..151324901-chr1:151370589..151373551,2	MCF-7	breast:
5	chr1:151043012..151044915-chr1:151322550..151324418,2	MCF-7	breast:
6	chr1:151323998..151326554-chr1:151327996..151330096,2	K562	blood:
7	chr1:151298654..151301594-chr1:151321885..151324849,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
RFX5	TF binding region
ENSG00000159377	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143390	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12409654	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1752385	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1780582	0.84[ASN][1000 genomes]
rs2025900	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2769266	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2769267	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2769268	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2769273	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800946	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2800947	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2800948	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2800949	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2800950	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2800951	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2800952	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv438026	chr1:151318733-151344703	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151320600-151326800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:151320800-151324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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