Variant report

Variant	rs4858940
Chromosome Location	chr3:88254820-88254821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1006896	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs10858	0.80[ASN][1000 genomes]
rs11925988	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493327	1.00[JPT][hapmap]
rs13074910	0.90[CEU][hapmap]
rs13317202	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2735556	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2735559	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4858934	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858939	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859003	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55928667	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55932154	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56185750	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56211058	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56246133	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6419868	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6419869	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551276	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551281	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551287	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551295	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132512	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73132546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73146085	0.80[ASN][1000 genomes]
rs73146095	0.80[ASN][1000 genomes]
rs73146099	0.80[ASN][1000 genomes]
rs7430022	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431968	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7432826	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7432838	1.00[JPT][hapmap]
rs7610494	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620576	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7620830	1.00[JPT][hapmap]
rs7624215	0.96[EUR][1000 genomes]
rs7650068	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9284814	0.92[EUR][1000 genomes]
rs9826925	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4858940	ZNF654	cis	lymphoblastoid	seeQTL
rs4858940	CGGBP1	cis	multi-tissue	Pritchard
rs4858940	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs4858940	LGALS14	trans	lymphoblastoid	seeQTL
rs4858940	CGGBP1	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88253400-88255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:88253400-88256200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:88253400-88278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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