Variant report

Variant	rs17135581
Chromosome Location	chr5:112709282-112709283
allele	C/T
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:41)

rs_ID	r²[population]
rs10038504	0.88[CHB][hapmap]
rs10040616	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043783	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs10053052	0.86[CHB][hapmap]
rs10053157	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs10053622	0.88[CHB][hapmap]
rs10055327	0.88[CHB][hapmap]
rs10057264	0.88[CHB][hapmap]
rs10063334	0.86[CHB][hapmap]
rs10066163	0.88[CHB][hapmap]
rs10066985	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952758	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs11960559	0.88[CHB][hapmap]
rs13157360	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162970	0.81[CEU][hapmap]
rs13182505	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13185592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354840	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs1353100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135618	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs255869	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs255875	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26965	0.81[CEU][hapmap]
rs34561076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3842916	0.86[CHB][hapmap]
rs3843501	0.86[CHB][hapmap]
rs3857436	0.86[CHB][hapmap]
rs41459745	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs4583882	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60702346	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879370	0.88[CHB][hapmap]
rs7701757	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7705430	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs7709550	0.88[CHB][hapmap]
rs7709818	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs7715884	0.88[CHB][hapmap]
rs7719254	0.82[CHB][hapmap]
rs7722421	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs7731564	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7737155	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs17135581	YTHDC2	cis	cerebellum	SCAN
rs17135581	MANBA	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112700800-112718000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:112707800-112719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:112708000-112709800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:112708000-112713800	Weak transcription	HMEC	breast
5	chr5:112708000-112714000	Weak transcription	NHEK	skin
6	chr5:112708000-112716200	Weak transcription	Fetal Kidney	kidney
7	chr5:112708600-112711200	Weak transcription	Fetal Stomach	stomach
8	chr5:112708600-112713400	Weak transcription	HUVEC	blood vessel
9	chr5:112708800-112711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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