Variant report

Variant	rs16868634
Chromosome Location	chr4:19594555-19594556
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10009708	0.95[EUR][1000 genomes]
rs10009772	0.81[ASN][1000 genomes]
rs10012861	0.82[ASN][1000 genomes]
rs10028337	0.81[ASN][1000 genomes]
rs10032188	0.81[ASN][1000 genomes]
rs10516334	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516337	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11933898	0.88[ASN][1000 genomes]
rs11939846	0.95[EUR][1000 genomes]
rs11940870	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11941599	0.82[ASN][1000 genomes]
rs11944084	0.83[ASN][1000 genomes]
rs11945412	0.82[ASN][1000 genomes]
rs13435279	0.95[EUR][1000 genomes]
rs16868608	0.90[ASN][1000 genomes]
rs16868686	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16868700	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16868774	0.95[EUR][1000 genomes]
rs16868777	0.92[EUR][1000 genomes]
rs16868779	0.88[EUR][1000 genomes]
rs28406392	0.82[ASN][1000 genomes]
rs28476561	0.95[EUR][1000 genomes]
rs28484795	0.87[EUR][1000 genomes]
rs28505527	0.81[ASN][1000 genomes]
rs28520510	0.91[EUR][1000 genomes]
rs28523873	0.95[EUR][1000 genomes]
rs28548641	0.95[EUR][1000 genomes]
rs28649741	0.95[EUR][1000 genomes]
rs28649908	0.82[ASN][1000 genomes]
rs28662302	0.82[ASN][1000 genomes]
rs28713269	0.82[ASN][1000 genomes]
rs3935063	0.87[EUR][1000 genomes]
rs3935613	0.87[EUR][1000 genomes]
rs4511994	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4541506	0.82[ASN][1000 genomes]
rs4637398	0.82[ASN][1000 genomes]
rs59810064	0.82[ASN][1000 genomes]
rs60069867	0.82[ASN][1000 genomes]
rs60284344	0.90[ASN][1000 genomes]
rs61356602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61359326	0.90[ASN][1000 genomes]
rs62295087	0.95[EUR][1000 genomes]
rs62295088	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62295089	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62295092	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62295093	0.88[EUR][1000 genomes]
rs62295094	0.86[EUR][1000 genomes]
rs62295096	0.87[EUR][1000 genomes]
rs62295097	0.87[EUR][1000 genomes]
rs62295103	0.87[EUR][1000 genomes]
rs62295105	0.87[EUR][1000 genomes]
rs62295106	0.87[EUR][1000 genomes]
rs62295109	0.87[EUR][1000 genomes]
rs62295136	0.87[EUR][1000 genomes]
rs62295149	0.87[EUR][1000 genomes]
rs62295150	0.87[EUR][1000 genomes]
rs62295152	0.82[EUR][1000 genomes]
rs62295155	0.82[EUR][1000 genomes]
rs62295156	0.82[EUR][1000 genomes]
rs62295158	0.81[EUR][1000 genomes]
rs62295159	0.81[EUR][1000 genomes]
rs62296084	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62296267	0.81[EUR][1000 genomes]
rs62296707	0.82[ASN][1000 genomes]
rs62296709	0.82[ASN][1000 genomes]
rs62296884	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62296886	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62296888	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62299872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62299873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823430	0.92[EUR][1000 genomes]
rs6837423	0.82[ASN][1000 genomes]
rs73097402	0.82[ASN][1000 genomes]
rs73099604	0.82[ASN][1000 genomes]
rs73099613	0.82[ASN][1000 genomes]
rs73099658	0.82[ASN][1000 genomes]
rs73099698	0.90[ASN][1000 genomes]
rs73101116	0.90[ASN][1000 genomes]
rs73101119	0.90[ASN][1000 genomes]
rs7659519	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7673978	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9291405	0.95[EUR][1000 genomes]
rs9990468	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878732	chr4:19172031-19660947	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv878733	chr4:19335464-19928602	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv878734	chr4:19474680-19598710	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv461286	chr4:19488871-19709795	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv593786	chr4:19488871-19709795	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv829873	chr4:19582263-19742515	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1001485	chr4:19585423-19655316	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16868634	LAP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:19594000-19594600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:19594000-19594800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:19594200-19594600	Enhancers	Hela-S3	cervix

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