Variant report

Variant	rs27566
Chromosome Location	chr5:112739130-112739131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10042223	0.81[CHB][hapmap]
rs10051834	0.81[CHB][hapmap]
rs10067046	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs10071966	0.84[CEU][hapmap]
rs10072511	0.84[CEU][hapmap]
rs10074214	0.81[CHB][hapmap]
rs10076501	0.84[CEU][hapmap]
rs1038918	0.83[CEU][hapmap]
rs10900684	0.84[CEU][hapmap]
rs11241200	0.84[CEU][hapmap]
rs1132528	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap]
rs11948072	0.86[CEU][hapmap]
rs12659978	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs13153071	0.84[CEU][hapmap]
rs13188946	0.81[CHB][hapmap]
rs13190054	0.85[AMR][1000 genomes]
rs1517206	0.84[CEU][hapmap]
rs1517208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1517210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154039	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154040	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164251	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs164253	0.85[AFR][1000 genomes]
rs171181	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17327526	0.83[LWK][hapmap]
rs173903	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820056	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs182987	0.81[AFR][1000 genomes]
rs1838207	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs1845290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs190453	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2222144	0.81[CHB][hapmap]
rs2303717	0.81[JPT][hapmap]
rs2416282	0.84[ASW][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap]
rs2416310	0.84[CEU][hapmap]
rs2434664	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2434665	0.84[CEU][hapmap]
rs255856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255863	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs255867	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs255874	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26960	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26983	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs26985	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs26987	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs26988	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27567	0.81[CHB][hapmap]
rs27700	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2910018	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs348927	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs348933	0.81[AFR][1000 genomes]
rs348949	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs348950	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs348953	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36612	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763139	0.94[JPT][hapmap]
rs3857435	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3906371	0.88[MEX][hapmap]
rs3936062	0.83[CEU][hapmap]
rs406288	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs423089	0.88[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4324667	0.88[AMR][1000 genomes]
rs4331889	0.81[CHB][hapmap]
rs4398627	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs4415069	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs459428	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs461034	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs463216	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4639215	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap]
rs465898	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs466564	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705812	0.84[CEU][hapmap]
rs4705813	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705830	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs4705831	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs485210	0.84[ASW][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap]
rs492346	0.84[ASW][hapmap];0.96[MEX][hapmap]
rs6594700	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6594704	0.81[CHB][hapmap]
rs6594705	0.81[CHB][hapmap]
rs6594710	0.81[CHB][hapmap]
rs6594711	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6594712	0.81[CHB][hapmap]
rs675353	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6867397	0.81[CHB][hapmap]
rs6869097	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6873400	0.87[CEU][hapmap]
rs6875238	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6879612	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6881976	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs6894434	0.84[CEU][hapmap]
rs7702120	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708084	0.81[CHB][hapmap]
rs7715342	0.85[AMR][1000 genomes]
rs7722276	0.86[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes]
rs7725589	0.81[CHB][hapmap]
rs7727449	0.87[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap]
rs7731465	0.81[CHB][hapmap]
rs7735247	0.83[CEU][hapmap]
rs9326895	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap]
rs9552	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs9686772	0.84[EUR][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs27566	YTHDC2	cis	cerebellum	SCAN
rs27566	LILRP2	trans	parietal	SCAN
rs27566	YTHDC2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112724400-112751200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:112734400-112739200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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