Variant report

Variant	rs602842
Chromosome Location	chr6:150685999-150686000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:150685960-150686110	GM12872	blood:	n/a	chr6:150685988-150685998
2	CTCF	chr6:150685918-150686010	MCF-7	breast:	n/a	chr6:150685988-150685998
3	CTCF	chr6:150685980-150686130	HEK293	kidney:	n/a	chr6:150685988-150685998

Variant related genes	Relation type
IYD	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11969964	0.93[JPT][hapmap]
rs1339110	0.86[JPT][hapmap]
rs1556881	0.80[JPT][hapmap]
rs2076287	0.80[JPT][hapmap]
rs2076288	0.80[JPT][hapmap]
rs2076289	0.80[JPT][hapmap]
rs2076290	0.80[JPT][hapmap]
rs2076291	0.80[JPT][hapmap]
rs2076292	0.80[JPT][hapmap]
rs3734734	0.80[JPT][hapmap]
rs3823259	0.80[JPT][hapmap]
rs4407723	0.80[JPT][hapmap]
rs5029121	0.80[JPT][hapmap]
rs612200	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs617594	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs618514	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62432478	0.81[ASN][1000 genomes]
rs629163	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs630632	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs632337	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs632829	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs640139	0.89[CEU][hapmap]
rs652210	0.87[EUR][1000 genomes]
rs653588	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs654101	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs654476	0.94[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs657961	0.82[CEU][hapmap]
rs660382	0.89[CEU][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs667815	0.82[CEU][hapmap]
rs671675	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs674414	0.82[CEU][hapmap]
rs683255	0.89[CEU][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7761373	0.93[JPT][hapmap]
rs7761906	0.80[JPT][hapmap]
rs9384445	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9397292	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9397303	0.80[JPT][hapmap]
rs9397944	0.80[JPT][hapmap]
rs9480323	0.87[EUR][1000 genomes];0.82[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	nsv830843	chr6:150517411-150691173	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2763602	chr6:150581193-150720666	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs602842	PPP1R14C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150684600-150686400	Weak transcription	Ovary	ovary

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