Variant report

Variant	rs6882900
Chromosome Location	chr5:112789573-112789574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112782163..112784363-chr5:112787985..112789693,2	K562	blood:
2	chr5:112789508..112791643-chr5:112823212..112825558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10428666	0.82[ASN][1000 genomes]
rs1116547	0.86[ASN][1000 genomes]
rs11241201	0.86[ASN][1000 genomes]
rs11241206	0.86[ASN][1000 genomes]
rs11241209	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11738075	0.86[ASN][1000 genomes]
rs11738215	0.86[ASN][1000 genomes]
rs11747924	0.85[EUR][1000 genomes]
rs11748503	0.82[ASN][1000 genomes]
rs11748794	0.80[EUR][1000 genomes]
rs12152879	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12519323	0.81[EUR][1000 genomes]
rs12519753	0.86[ASN][1000 genomes]
rs12519818	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12520003	0.84[ASN][1000 genomes]
rs12523255	0.86[ASN][1000 genomes]
rs1517209	0.86[ASN][1000 genomes]
rs1586943	0.86[ASN][1000 genomes]
rs17135597	0.86[ASN][1000 genomes]
rs17135608	0.84[ASN][1000 genomes]
rs17135616	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17135630	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17135753	0.81[EUR][1000 genomes]
rs1833678	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1850410	0.86[ASN][1000 genomes]
rs2042222	0.86[EUR][1000 genomes]
rs2416281	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3846722	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4122546	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705551	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705814	0.86[ASN][1000 genomes]
rs4705817	0.86[ASN][1000 genomes]
rs4705818	0.88[ASN][1000 genomes]
rs4705819	0.88[ASN][1000 genomes]
rs57077871	0.80[EUR][1000 genomes]
rs66490974	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66497221	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66502937	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs66583752	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs66728961	0.86[ASN][1000 genomes]
rs67020702	0.81[EUR][1000 genomes]
rs67103739	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67268709	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs67303814	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs67723806	0.81[EUR][1000 genomes]
rs67764628	0.82[ASN][1000 genomes]
rs6861786	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864528	0.84[ASN][1000 genomes]
rs6878001	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6879800	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6883441	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6896469	0.82[EUR][1000 genomes]
rs6896501	0.82[EUR][1000 genomes]
rs72792179	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72794121	0.82[EUR][1000 genomes]
rs73236478	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73236479	0.92[ASN][1000 genomes]
rs73241779	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73242809	0.81[EUR][1000 genomes]
rs73247445	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7702833	0.82[EUR][1000 genomes]
rs7707443	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957777	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9800316	0.86[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6882900	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112782200-112789600	Enhancers	Fetal Stomach	stomach
2	chr5:112786200-112810000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112786600-112790800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:112788000-112794200	Weak transcription	NHEK	skin
5	chr5:112788000-112808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:112788200-112807600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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