Variant report

Variant	rs6878001
Chromosome Location	chr5:112813100-112813101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112812370..112815012-chr5:112823998..112826646,2	K562	blood:
2	chr5:112809363..112813589-chr5:112821986..112825015,5	MCF-7	breast:
3	chr5:112811062..112815504-chr5:112818708..112822151,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap]
rs10071816	0.94[CEU][hapmap]
rs10079895	0.94[CEU][hapmap]
rs10079973	0.94[CEU][hapmap]
rs10080096	0.89[CEU][hapmap]
rs10428666	0.85[JPT][hapmap]
rs10477497	0.88[CEU][hapmap]
rs10478127	0.94[CEU][hapmap]
rs10900685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1116547	0.88[JPT][hapmap];0.81[MEX][hapmap]
rs11241201	0.88[JPT][hapmap];0.81[MEX][hapmap]
rs11241206	0.88[JPT][hapmap];0.85[MEX][hapmap]
rs11241214	0.94[CEU][hapmap]
rs11241215	0.88[CEU][hapmap]
rs11738075	0.88[JPT][hapmap]
rs11738215	0.88[JPT][hapmap];0.85[MEX][hapmap]
rs11741963	0.82[ASN][1000 genomes]
rs11747924	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11748145	0.86[EUR][1000 genomes]
rs11748794	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap]
rs11750945	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11956399	0.94[CEU][hapmap]
rs12186798	0.94[CEU][hapmap]
rs12514091	0.88[JPT][hapmap]
rs12516418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12519323	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12519818	0.89[ASN][1000 genomes]
rs12523255	0.85[JPT][hapmap]
rs12660001	0.94[CEU][hapmap]
rs1443683	0.86[JPT][hapmap]
rs17135597	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17135608	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17135616	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs17135630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs17135753	1.00[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17135754	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1833678	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850410	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2042222	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2068923	0.88[JPT][hapmap]
rs2288449	0.94[CEU][hapmap]
rs2416281	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763140	0.94[CEU][hapmap]
rs3815911	0.94[CEU][hapmap]
rs3846721	0.86[ASW][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap]
rs3846722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936061	0.94[CEU][hapmap]
rs4122546	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4334877	0.88[CEU][hapmap]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705814	0.88[JPT][hapmap]
rs4705817	0.86[JPT][hapmap]
rs4705819	0.85[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57077871	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6594734	0.94[CEU][hapmap]
rs66490974	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66497221	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66502937	0.89[ASN][1000 genomes]
rs66583752	0.89[ASN][1000 genomes]
rs66644309	0.82[ASN][1000 genomes]
rs67020702	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67103739	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67268709	0.89[ASN][1000 genomes]
rs67723806	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859688	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6861786	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6864369	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6864528	0.88[JPT][hapmap];0.85[MEX][hapmap]
rs6877432	0.89[CEU][hapmap]
rs6877524	0.88[JPT][hapmap]
rs6879800	0.93[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs6882900	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs6883441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6886628	0.94[CEU][hapmap]
rs6889574	0.94[CEU][hapmap]
rs6896469	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6896501	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898425	0.81[CEU][hapmap]
rs72792179	0.89[ASN][1000 genomes]
rs72794121	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72805465	0.82[EUR][1000 genomes]
rs73241779	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73242809	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73247445	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7349799	0.87[CEU][hapmap]
rs7702833	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706958	0.94[CEU][hapmap]
rs7707443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap]
rs7711367	0.94[CEU][hapmap]
rs7717000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7729433	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7737023	0.94[CEU][hapmap]
rs919304	0.94[CEU][hapmap]
rs9326893	0.94[CEU][hapmap]
rs957777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6878001	YTHDC2	cis	parietal	SCAN
rs6878001	YTHDC2	cis	multi-tissue	Pritchard
rs6878001	YTHDC2	cis	cerebellum	SCAN
rs6878001	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL
rs6878001	DCP2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112807800-112821600	Weak transcription	HMEC	breast
2	chr5:112810200-112823000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:112810400-112820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112810400-112821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112810600-112813200	Weak transcription	Fetal Heart	heart
6	chr5:112811800-112813400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:112812800-112815800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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