Variant report

Variant	rs3909887
Chromosome Location	chr5:112838128-112838129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112838066..112839571-chr5:112849174..112852055,2	MCF-7	breast:
2	chr5:112822923..112824962-chr5:112838112..112840774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10036298	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10036300	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10038632	0.86[ASN][1000 genomes]
rs10039853	0.92[ASN][1000 genomes]
rs10040203	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10040430	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10040516	0.84[EUR][1000 genomes]
rs10042563	0.84[EUR][1000 genomes]
rs10043066	0.84[EUR][1000 genomes]
rs10046057	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10052077	0.84[EUR][1000 genomes]
rs10053582	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10061552	0.88[ASN][1000 genomes]
rs10063008	0.87[ASN][1000 genomes]
rs10065616	0.84[EUR][1000 genomes]
rs10071816	0.92[ASN][1000 genomes]
rs10072547	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076131	0.84[EUR][1000 genomes]
rs10079603	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10079758	0.92[ASN][1000 genomes]
rs10079895	0.92[ASN][1000 genomes]
rs10079973	0.92[ASN][1000 genomes]
rs10080096	0.92[ASN][1000 genomes]
rs1017209	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035888	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10477495	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10477497	0.92[ASN][1000 genomes]
rs10477498	0.92[ASN][1000 genomes]
rs10477499	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10477500	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10478126	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478127	0.92[ASN][1000 genomes]
rs10478129	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10478132	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1052896	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1080858	0.84[EUR][1000 genomes]
rs11241210	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11241211	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241214	0.88[ASN][1000 genomes]
rs11241215	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11742968	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11749931	0.92[ASN][1000 genomes]
rs11750449	0.85[EUR][1000 genomes]
rs11750488	0.86[EUR][1000 genomes]
rs11956399	0.92[ASN][1000 genomes]
rs12186798	0.92[ASN][1000 genomes]
rs12514105	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12516911	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12523145	0.83[AMR][1000 genomes]
rs12652172	0.92[ASN][1000 genomes]
rs12654189	0.92[ASN][1000 genomes]
rs12660001	0.92[ASN][1000 genomes]
rs13359625	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359648	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359652	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359703	0.88[ASN][1000 genomes]
rs13362066	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549628	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135766	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135776	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1820059	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833680	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833681	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862315	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970798	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115216	0.83[EUR][1000 genomes]
rs2162842	0.92[ASN][1000 genomes]
rs2162847	0.83[EUR][1000 genomes]
rs2288449	0.86[ASN][1000 genomes]
rs2416319	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28558374	0.92[ASN][1000 genomes]
rs28848005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2900072	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34514665	0.95[ASN][1000 genomes]
rs34864074	0.95[ASN][1000 genomes]
rs35162738	0.95[ASN][1000 genomes]
rs35526509	0.91[ASN][1000 genomes]
rs3763138	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3763140	0.87[ASN][1000 genomes]
rs3815911	0.85[ASN][1000 genomes]
rs3842917	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3857437	0.86[AFR][1000 genomes]
rs3906371	0.86[AFR][1000 genomes]
rs3906538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3936061	0.95[ASN][1000 genomes]
rs4122547	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4132093	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4132094	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4334877	0.95[ASN][1000 genomes]
rs4588592	0.87[ASN][1000 genomes]
rs4705552	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705553	0.94[ASN][1000 genomes]
rs4705555	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705556	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705557	0.86[ASN][1000 genomes]
rs4705823	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705825	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705827	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705828	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705832	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705833	0.88[EUR][1000 genomes]
rs56030143	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56206672	0.86[ASN][1000 genomes]
rs57134656	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58044020	0.92[ASN][1000 genomes]
rs58391392	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60265545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60871281	0.92[ASN][1000 genomes]
rs60914066	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6594718	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6594719	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594720	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594721	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594729	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594732	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594733	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594734	0.92[ASN][1000 genomes]
rs6594738	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67915940	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865809	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6867502	0.86[ASN][1000 genomes]
rs6876448	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6877432	0.92[ASN][1000 genomes]
rs6877466	0.86[ASN][1000 genomes]
rs6877834	0.86[ASN][1000 genomes]
rs6878282	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6878355	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6878900	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6880447	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6883383	0.87[ASN][1000 genomes]
rs6883557	0.87[ASN][1000 genomes]
rs6886628	0.88[ASN][1000 genomes]
rs6887816	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6889501	0.92[ASN][1000 genomes]
rs6889574	0.92[ASN][1000 genomes]
rs6889783	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898425	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72805422	0.92[ASN][1000 genomes]
rs7349799	0.90[ASN][1000 genomes]
rs754573	0.85[EUR][1000 genomes]
rs7701913	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7706215	0.92[ASN][1000 genomes]
rs7706796	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7706958	0.92[ASN][1000 genomes]
rs7707895	0.85[EUR][1000 genomes]
rs7709110	0.84[ASN][1000 genomes]
rs7711078	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7711211	0.92[ASN][1000 genomes]
rs7711367	0.92[ASN][1000 genomes]
rs7713038	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7713348	0.83[AFR][1000 genomes]
rs7713451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7713846	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7715601	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7717644	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7722918	0.86[ASN][1000 genomes]
rs7723108	0.86[EUR][1000 genomes]
rs7729306	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7730532	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730557	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730949	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7732310	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7737023	0.92[ASN][1000 genomes]
rs919304	0.87[ASN][1000 genomes]
rs929774	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326893	0.88[ASN][1000 genomes]
rs9326897	0.84[EUR][1000 genomes]
rs9654519	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885245	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3909887	YTHDC2	cis	multi-tissue	Pritchard
rs3909887	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112827200-112840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:112838000-112839000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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