Variant report

Variant	rs2472304
Chromosome Location	chr15:75044238-75044239
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75043196..75045391-chr15:75075402..75077625,2	K562	blood:
2	chr15:75037842..75040616-chr15:75043779..75046442,3	K562	blood:
3	chr15:74929455..74931233-chr15:75042400..75045089,2	K562	blood:
4	chr15:75008936..75010510-chr15:75042594..75044929,2	K562	blood:
5	chr15:75041437..75045142-chr15:75051536..75054125,3	K562	blood:
6	chr15:74932436..74935063-chr15:75043587..75046477,2	MCF-7	breast:
7	chr15:75035073..75037761-chr15:75042329..75044643,2	MCF-7	breast:
8	chr15:74918395..74921353-chr15:75041999..75044301,2	MCF-7	breast:
9	chr15:75042997..75044715-chr15:75054154..75056433,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11072507	0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072508	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11630478	0.84[AMR][1000 genomes]
rs11632414	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635664	0.82[AMR][1000 genomes]
rs11854147	0.83[CEU][hapmap]
rs12591513	0.84[AMR][1000 genomes]
rs12594062	0.84[AMR][1000 genomes]
rs12898997	0.82[AMR][1000 genomes]
rs12903541	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12903896	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905199	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12909307	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1378940	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378941	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378942	0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2168518	0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470890	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472299	0.80[CEU][hapmap]
rs2960192	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34862454	0.84[AMR][1000 genomes]
rs35206230	0.84[AMR][1000 genomes]
rs3784789	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886410	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs762551	0.80[CEU][hapmap]

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	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

Variant related diseases (count:1)

Disease	PMID	Source
Caffeine consumption	21490707	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2472304	TMEM202	cis	parietal	SCAN
rs2472304	SCAMP2	cis	parietal	SCAN
rs2472304	SCAMP5	cis	cerebellum	SCAN
rs2472304	SCAMP5	cis	Artery Tibial	GTEx
rs2472304	CPLX3	cis	parietal	SCAN
rs2472304	CSK	cis	lymphoblastoid	seeQTL
rs2472304	MPI	cis	lymphoblastoid	seeQTL
rs2472304	SCAMP5	cis	lung	GTEx
rs2472304	COX5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75040600-75044600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:75041200-75044400	Flanking Active TSS	Liver	Liver
3	chr15:75041600-75044800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:75042400-75044600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:75043400-75045800	Enhancers	Placenta	Placenta
6	chr15:75043600-75044600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:75043600-75045600	Enhancers	Lung	lung
8	chr15:75043600-75046000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr15:75043800-75051200	Weak transcription	HepG2	liver
10	chr15:75044200-75044800	Active TSS	Spleen	Spleen
11	chr15:75044200-75045000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr15:75044200-75045600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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