Variant report

Variant	rs12595284
Chromosome Location	chr15:51655762-51655763
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51627940..51629861-chr15:51655726..51658198,2	MCF-7	breast:
2	chr15:51651683..51656277-chr15:51657085..51661160,7	MCF-7	breast:
3	chr15:51654951..51657381-chr15:51671722..51675583,3	K562	blood:

Variant related genes	Relation type
ENSG00000259194	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11070846	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439026	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17647970	0.92[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1808141	0.88[CEU][hapmap]
rs1870048	0.81[ASN][1000 genomes]
rs2445778	0.86[JPT][hapmap]
rs2445779	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2446411	0.86[JPT][hapmap]
rs2446427	0.85[JPT][hapmap]
rs2470171	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470172	0.81[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470173	0.86[JPT][hapmap]
rs2470184	0.86[JPT][hapmap]
rs2470186	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2470189	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35463563	0.84[EUR][1000 genomes]
rs35754161	0.83[EUR][1000 genomes]
rs36064983	0.81[EUR][1000 genomes]
rs4774588	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs4775940	0.88[CEU][hapmap]
rs4775942	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58010613	0.83[EUR][1000 genomes]
rs7173573	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8031311	0.92[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs930921	0.87[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12595284	SPPL2A	cis	parietal	SCAN
rs12595284	SLC28A2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51640800-51676200	Weak transcription	Aorta	Aorta
2	chr15:51647200-51659800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:51649600-51660600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:51649800-51657800	Weak transcription	Stomach Mucosa	stomach
5	chr15:51652600-51659000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:51652800-51659400	Weak transcription	Esophagus	oesophagus
7	chr15:51653600-51658400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:51654400-51656000	Enhancers	Placenta	Placenta
9	chr15:51655000-51656600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr15:51655000-51657400	Enhancers	Brain Substantia Nigra	brain
11	chr15:51655200-51655800	Enhancers	Brain Hippocampus Middle	brain
12	chr15:51655200-51656800	Enhancers	Brain Angular Gyrus	brain
13	chr15:51655400-51655800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:51655600-51656000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:51655600-51656000	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:51655600-51656400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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