Variant report

Variant	rs2317248
Chromosome Location	chr3:56739579-56739580
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1387713	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565376	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1565377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1844477	0.82[ASN][1000 genomes]
rs2317246	0.82[AMR][1000 genomes]
rs3821413	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs4273342	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4407379	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4455300	0.87[EUR][1000 genomes]
rs4634082	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681725	0.81[MEX][hapmap]
rs4681763	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681765	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681767	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445820	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772854	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6773823	0.84[ASN][1000 genomes]
rs6773931	0.84[ASN][1000 genomes]
rs6805910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807177	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628922	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7629016	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857253	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2317248	C3orf51	cis	cerebellum	SCAN
rs2317248	ARHGEF3	cis	cerebellum	SCAN
rs2317248	CCDC66	cis	parietal	SCAN
rs2317248	CCDC66	cis	lymphoblastoid	seeQTL
rs2317248	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL
rs2317248	CCDC66	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56734800-56756400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:56736400-56740000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr3:56738600-56739600	Enhancers	Primary T cells from cord blood	blood
4	chr3:56738600-56739600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:56738600-56739600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:56738600-56739600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:56738600-56739800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:56738600-56739800	Enhancers	GM12878-XiMat	blood
9	chr3:56739400-56758600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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