Variant report

Variant	rs2253520
Chromosome Location	chr13:48857954-48857955
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48857773..48861171-chr13:48869785..48872052,3	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10219833	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12583516	0.85[ASN][1000 genomes]
rs12871662	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12871740	0.93[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573601	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886795	0.92[EUR][1000 genomes]
rs1894255	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs1925744	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925745	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1951775	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1981434	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs1981435	0.82[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs198584	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs198590	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs198604	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs198607	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs198612	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs198619	0.90[CEU][hapmap]
rs198634	0.92[ASN][1000 genomes]
rs2243461	0.91[EUR][1000 genomes]
rs2243626	0.85[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2251813	0.92[EUR][1000 genomes]
rs2254423	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2406933	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854345	0.91[ASN][1000 genomes]
rs34217484	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803188	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818455	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs399413	0.83[TSI][hapmap]
rs4151450	0.90[CEU][hapmap];0.86[TSI][hapmap]
rs4151520	0.84[ASN][1000 genomes]
rs4594153	0.94[EUR][1000 genomes]
rs4600372	0.91[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs61973349	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7358982	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7984554	0.93[EUR][1000 genomes]
rs7984795	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs7999447	0.93[EUR][1000 genomes]
rs8001315	0.93[EUR][1000 genomes]
rs9316367	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316369	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526465	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9526466	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526470	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526475	0.83[TSI][hapmap]
rs9534998	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535000	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535002	0.92[EUR][1000 genomes]
rs9535003	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535007	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9535009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535011	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535032	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9562815	0.82[ASN][1000 genomes]
rs9568025	0.85[ASN][1000 genomes]
rs9568026	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568027	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568028	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568029	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9568032	0.92[ASN][1000 genomes]
rs9568033	0.92[ASN][1000 genomes]
rs9568034	0.92[ASN][1000 genomes]
rs9568035	0.83[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2253520	ITM2B	cis	lymphoblastoid	seeQTL
rs2253520	LPAR6	cis	parietal	SCAN
rs2253520	ATAD2	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48844400-48877200	Weak transcription	Aorta	Aorta
2	chr13:48853400-48860400	Weak transcription	Brain Substantia Nigra	brain
3	chr13:48857600-48858000	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links