Variant report

Variant	rs4398627
Chromosome Location	chr5:112765920-112765921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10036300	0.94[YRI][hapmap]
rs10037429	0.94[YRI][hapmap]
rs1132528	0.84[MEX][hapmap]
rs11744710	0.94[YRI][hapmap]
rs11744737	0.94[YRI][hapmap]
rs11948187	0.87[YRI][hapmap]
rs11948437	0.89[YRI][hapmap]
rs11948446	0.83[YRI][hapmap]
rs11949669	0.89[YRI][hapmap]
rs11953906	0.83[YRI][hapmap]
rs11955591	0.83[YRI][hapmap]
rs13161610	0.83[YRI][hapmap]
rs13161969	0.80[YRI][hapmap]
rs1517210	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs164251	0.93[CHB][hapmap]
rs164252	1.00[YRI][hapmap]
rs182988	0.89[YRI][hapmap]
rs1838207	0.80[CHB][hapmap]
rs1845290	0.93[CHB][hapmap]
rs255856	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs26985	0.87[CHB][hapmap];0.83[AMR][1000 genomes]
rs26987	0.84[AMR][1000 genomes]
rs26988	0.85[AMR][1000 genomes]
rs27566	0.93[CHB][hapmap];0.92[CHD][hapmap]
rs2914152	0.83[YRI][hapmap]
rs348939	0.95[YRI][hapmap]
rs3763141	0.83[YRI][hapmap]
rs3857435	0.87[CHB][hapmap]
rs3857437	0.85[JPT][hapmap]
rs3906371	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs423089	0.93[CHB][hapmap]
rs4324667	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459428	0.87[CHB][hapmap]
rs461034	0.93[CHB][hapmap];0.83[YRI][hapmap]
rs463216	0.93[CHB][hapmap]
rs4639215	0.84[MEX][hapmap]
rs465898	0.93[CHB][hapmap]
rs466564	0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs6594711	0.87[CHB][hapmap]
rs675353	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs6869097	0.93[CHB][hapmap]
rs7702120	0.87[CHB][hapmap]
rs7722276	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs7727449	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731164	0.81[YRI][hapmap]
rs9326895	0.84[MEX][hapmap]
rs9552	0.83[MEX][hapmap]

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
rs4398627	YTHDC2	cis	cerebellum	SCAN
rs4398627	YTHDC2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112762000-112786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112764400-112769400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112764400-112779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112764600-112786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112764800-112769000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:112764800-112786800	Weak transcription	NHEK	skin

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