Variant report

Variant	rs28875897
Chromosome Location	chr15:51575659-51575660
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	CTCF	chr15:51575540-51575690	GM12867	blood:	n/a	n/a
2	SPI1	chr15:51574975-51575778	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:51568163..51571047-chr15:51573352..51576170,3	MCF-7	breast:
2	chr15:51570765..51572650-chr15:51575389..51576979,2	MCF-7	breast:
3	chr15:51574618..51575812-chr15:51673135..51674386,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259701	TF binding region
ENSG00000137869	Chromatin interaction
ENSG00000259701	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12101420	1.00[AFR][1000 genomes]
rs12101421	1.00[AFR][1000 genomes]
rs28367445	0.85[AFR][1000 genomes]
rs28393393	0.85[AFR][1000 genomes]
rs28403244	1.00[AFR][1000 genomes]
rs28427432	1.00[AFR][1000 genomes]
rs28430977	1.00[AFR][1000 genomes]
rs28460528	1.00[AFR][1000 genomes]
rs28463224	0.87[AFR][1000 genomes]
rs28465243	1.00[AFR][1000 genomes]
rs28524029	1.00[AFR][1000 genomes]
rs28604459	1.00[AFR][1000 genomes]
rs28648895	1.00[AFR][1000 genomes]
rs28685202	1.00[AFR][1000 genomes]
rs28693825	1.00[AFR][1000 genomes]
rs28703085	1.00[AFR][1000 genomes]
rs28730382	1.00[AFR][1000 genomes]
rs74013181	1.00[AFR][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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	esv3398984	chr15:51574559-51577866	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51574400-51576200	Enhancers	Primary B cells from peripheral blood	blood
2	chr15:51574600-51576600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:51574800-51576000	Enhancers	Primary B cells from cord blood	blood
4	chr15:51575000-51575800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr15:51575000-51575800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:51575000-51575800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:51575000-51576000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:51575000-51576000	Active TSS	Brain Anterior Caudate	brain
9	chr15:51575000-51577800	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:51575000-51578600	Weak transcription	HepG2	liver
11	chr15:51575000-51580400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:51575000-51580400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:51575000-51580400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:51575000-51580400	Weak transcription	NHDF-Ad	bronchial
15	chr15:51575200-51578400	Strong transcription	Placenta	Placenta
16	chr15:51575200-51579400	Weak transcription	Stomach Mucosa	stomach
17	chr15:51575200-51580600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:51575200-51580600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:51575400-51575800	Active TSS	Brain Hippocampus Middle	brain
20	chr15:51575400-51576200	Weak transcription	Osteobl	bone
21	chr15:51575400-51579600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:51575600-51575800	Enhancers	Adipose Nuclei	Adipose
23	chr15:51575600-51575800	Enhancers	Brain Cingulate Gyrus	brain
24	chr15:51575600-51576000	Enhancers	GM12878-XiMat	blood

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