Variant report

Variant	rs6876848
Chromosome Location	chr5:112681830-112681831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10042223	0.92[CHB][hapmap]
rs10051115	0.82[CEU][hapmap]
rs10051834	0.92[CHB][hapmap]
rs10074214	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs13181534	0.82[CEU][hapmap]
rs13188946	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs1366393	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1850407	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1850412	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs2222144	0.92[CHB][hapmap]
rs26959	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs26961	0.86[CHB][hapmap]
rs26966	0.85[CHB][hapmap]
rs27567	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs4331889	0.92[CHB][hapmap]
rs6594701	1.00[CHB][hapmap]
rs6594704	0.92[CHB][hapmap]
rs6594705	0.92[CHB][hapmap]
rs6594710	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs6594712	0.92[CHB][hapmap]
rs6594713	0.82[CEU][hapmap]
rs6594714	0.82[CEU][hapmap]
rs6867397	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs6868141	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868148	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6870401	0.82[CEU][hapmap]
rs6880552	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887482	0.82[CEU][hapmap]
rs6894687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708084	0.92[CHB][hapmap]
rs7714760	0.89[CEU][hapmap]
rs7717422	0.86[CHB][hapmap]
rs7725589	0.92[CHB][hapmap]
rs7729269	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs7731231	0.82[CEU][hapmap]
rs7731465	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs9326886	0.86[CHB][hapmap]
rs9326887	0.85[CHB][hapmap]
rs9326888	0.86[CHB][hapmap]
rs9687632	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6876848	YTHDC2	cis	parietal	SCAN
rs6876848	YTHDC2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112678800-112682400	Enhancers	HMEC	breast
3	chr5:112679000-112682000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112679800-112683000	Weak transcription	Fetal Stomach	stomach
5	chr5:112680400-112682000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112680600-112682000	Enhancers	NHEK	skin

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