Variant report

Variant	rs12439740
Chromosome Location	chr15:53027291-53027292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52969340..52972976-chr15:53024542..53030044,12	MCF-7	breast:
2	chr15:52623157..52624688-chr15:53027206..53029012,2	MCF-7	breast:
3	chr15:52859015..52862196-chr15:53026182..53028979,3	MCF-7	breast:
4	chr15:52965949..52968646-chr15:53025332..53028243,3	MCF-7	breast:
5	chr15:53022444..53024405-chr15:53025609..53027744,2	MCF-7	breast:
6	chr15:52548183..52549192-chr15:53027141..53028320,9	K562	blood:
7	chr15:52819938..52821534-chr15:53026653..53028952,2	MCF-7	breast:
8	chr15:52968697..52973342-chr15:53018163..53028590,24	MCF-7	breast:
9	chr15:52508008..52509939-chr15:53026331..53028847,2	MCF-7	breast:
10	chr15:53001338..53004194-chr15:53026134..53027960,2	MCF-7	breast:
11	chr15:52623273..52624277-chr15:53027279..53028330,7	MCF-7	breast:
12	chr15:53020023..53021825-chr15:53025584..53028001,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000197535	Chromatin interaction
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12437633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12437652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439014	0.83[AMR][1000 genomes]
rs12440398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17652272	0.83[AMR][1000 genomes]
rs74014119	1.00[EUR][1000 genomes]
rs7496443	1.00[EUR][1000 genomes]
rs8037939	1.00[EUR][1000 genomes]
rs8038634	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049055	chr15:52990467-53030603	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1035212	chr15:52995637-53030603	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1049144	chr15:52995637-53039179	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1049619	chr15:52995637-53041887	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv569425	chr15:53001538-53038488	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv569426	chr15:53014003-53046210	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv514782	chr15:53026224-53027764	Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53022800-53029800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:53024000-53030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:53024200-53028400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:53026000-53030400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:53026000-53037400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:53026200-53027600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:53026200-53038200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:53026400-53029800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:53026400-53030000	Weak transcription	Osteobl	bone
10	chr15:53026600-53029400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:53026600-53030200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:53026800-53029400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:53026800-53029800	Weak transcription	NHDF-Ad	bronchial
14	chr15:53026800-53030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:53027000-53028000	Weak transcription	Liver	Liver
16	chr15:53027000-53030000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:53027200-53028200	Weak transcription	Adipose Nuclei	Adipose
18	chr15:53027200-53029800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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