Variant report

Variant	rs2472299
Chromosome Location	chr15:75033400-75033401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75032689..75033689-chr5:172197934..172198465,2	HCT-116	colon:
2	chr15:75032709..75033689-chr5:172197767..172198485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120129	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072502	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072504	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072505	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072506	0.81[EUR][1000 genomes]
rs11634474	0.81[CEU][hapmap]
rs11854147	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs12442901	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs12591078	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378938	0.82[CEU][hapmap]
rs1543927	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2168519	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs2301249	0.82[CEU][hapmap]
rs2445618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470890	0.80[CEU][hapmap]
rs2472298	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472304	0.80[CEU][hapmap]
rs4886406	0.86[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886629	0.82[CEU][hapmap]
rs55868854	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7085	0.82[CEU][hapmap]
rs762551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033381	0.82[CEU][hapmap];0.82[CHD][hapmap];0.86[TSI][hapmap]
rs936226	0.82[CEU][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2763106	chr15:75014464-75034186	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary heart disease	21378988	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2472299	SCAMP2	cis	parietal	SCAN
rs2472299	MPI	cis	parietal	SCAN
rs2472299	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs2472299	ULK3	cis	multi-tissue	Pritchard
rs2472299	MPI	cis	lymphoblastoid	seeQTL
rs2472299	SCAMP5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75019400-75033800	Weak transcription	Right Atrium	heart
2	chr15:75023800-75041600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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