Variant report

Variant	rs9284814
Chromosome Location	chr3:88273071-88273072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1006896	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11925988	0.92[EUR][1000 genomes]
rs13074910	1.00[CEU][hapmap]
rs13317202	0.92[EUR][1000 genomes]
rs1431154	0.80[YRI][hapmap]
rs2735556	1.00[CEU][hapmap]
rs2735559	1.00[CEU][hapmap]
rs4303891	0.90[ASW][hapmap];0.85[YRI][hapmap]
rs4443201	0.90[YRI][hapmap]
rs4858933	1.00[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap]
rs4858934	0.84[EUR][1000 genomes]
rs4858939	0.94[EUR][1000 genomes]
rs4858940	0.92[EUR][1000 genomes]
rs4859003	0.95[EUR][1000 genomes]
rs55928667	0.82[EUR][1000 genomes]
rs55932154	0.85[EUR][1000 genomes]
rs56185750	0.85[EUR][1000 genomes]
rs56211058	0.85[EUR][1000 genomes]
rs6419868	0.95[EUR][1000 genomes]
rs6419869	0.92[EUR][1000 genomes]
rs6551270	0.95[YRI][hapmap]
rs6551276	0.87[EUR][1000 genomes]
rs6551281	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6551287	0.90[EUR][1000 genomes]
rs6551295	0.94[EUR][1000 genomes]
rs73132512	0.85[EUR][1000 genomes]
rs73132546	0.85[EUR][1000 genomes]
rs7430022	0.92[EUR][1000 genomes]
rs7431968	1.00[CEU][hapmap]
rs7432751	0.84[AFR][1000 genomes]
rs7432826	0.87[EUR][1000 genomes]
rs7610494	0.95[EUR][1000 genomes]
rs7620576	0.91[EUR][1000 genomes]
rs7621357	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs7624215	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632965	0.84[AFR][1000 genomes]
rs7633486	0.94[AFR][1000 genomes]
rs7636845	0.90[YRI][hapmap]
rs7650068	0.92[EUR][1000 genomes]
rs9310073	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap]
rs9826925	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9865578	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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1013031	chr3:88256289-88347505	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9284814	CXCR4	trans	lymphoblastoid	seeQTL
rs9284814	CGGBP1	cis	uninvolved skin	skin_eQTL
rs9284814	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs9284814	ZNF654	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88253400-88278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:88268600-88274400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:88268600-88274400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:88271800-88279600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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