Variant report

Variant	rs28475336
Chromosome Location	chr15:75286967-75286968
allele	A/C
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	REST	chr15:75286443-75288128	HL-60	blood:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75286894-75286907 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
2	REST	chr15:75286914-75288263	A549	lung:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
3	REST	chr15:75286860-75288250	PFSK-1	brain:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75286894-75286907 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
4	REST	chr15:75286933-75287105	K562	blood:	n/a	n/a
5	REST	chr15:75286898-75287039	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:
2	chr15:75246590..75249281-chr15:75285572..75288569,4	MCF-7	breast:
3	chr15:75249195..75251408-chr15:75284576..75287402,2	K562	blood:
4	chr15:75247055..75248613-chr15:75284445..75287146,2	K562	blood:
5	chr15:75286466..75289268-chr15:75313854..75316191,2	MCF-7	breast:
6	chr15:75285958..75287550-chr15:75318167..75319943,2	MCF-7	breast:

Variant related genes	Relation type
SCAMP5	TF binding region
ENSG00000260483	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000178718	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs28624413	1.00[AMR][1000 genomes]
rs34882682	1.00[AMR][1000 genomes]
rs57201524	1.00[AMR][1000 genomes]
rs57292669	1.00[AMR][1000 genomes]
rs57703835	1.00[AMR][1000 genomes]
rs57961156	1.00[AMR][1000 genomes]
rs58881240	1.00[AMR][1000 genomes]
rs59072564	1.00[AMR][1000 genomes]
rs59430331	1.00[AMR][1000 genomes]
rs59434261	1.00[AMR][1000 genomes]
rs59507052	1.00[AMR][1000 genomes]
rs60318248	1.00[AMR][1000 genomes]
rs60555940	1.00[AMR][1000 genomes]
rs60568451	1.00[AMR][1000 genomes]
rs60910940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61398553	1.00[AMR][1000 genomes]
rs7173734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75283200-75287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:75283400-75287400	Weak transcription	HMEC	breast
3	chr15:75283400-75287400	Weak transcription	NHEK	skin
4	chr15:75283400-75287600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:75286200-75287000	Enhancers	Fetal Brain Male	brain
6	chr15:75286400-75287000	Active TSS	Brain Anterior Caudate	brain
7	chr15:75286400-75287400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:75286400-75287800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:75286600-75287400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:75286600-75287600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr15:75286600-75287600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:75286600-75287600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr15:75286600-75288400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:75286600-75289000	Active TSS	Brain Substantia Nigra	brain
15	chr15:75286600-75289600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr15:75286800-75287000	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr15:75286800-75287200	Active TSS	Fetal Brain Female	brain
18	chr15:75286800-75287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:75286800-75287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:75286800-75288600	Active TSS	Brain Cingulate Gyrus	brain
21	chr15:75286800-75288800	Active TSS	Brain Angular Gyrus	brain

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