Variant report

Variant	rs551607
Chromosome Location	chr1:179903031-179903032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179901208..179903781-chr1:179908885..179911377,2	K562	blood:
2	chr1:179901782..179903357-chr1:179905596..179908288,2	K562	blood:
3	chr1:179890511..179892011-chr1:179902778..179905230,2	MCF-7	breast:
4	chr1:179898573..179901417-chr1:179902522..179905124,2	MCF-7	breast:
5	chr1:179901208..179903839-chr1:179908885..179910627,2	K562	blood:

Variant related genes	Relation type
ENSG00000261831	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10913916	0.93[JPT][hapmap]
rs10913917	0.81[JPT][hapmap]
rs10913918	0.83[CEU][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12091685	0.82[CHD][hapmap]
rs1281384	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1281386	0.95[ASN][1000 genomes]
rs1281389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297205	0.93[JPT][hapmap]
rs2281805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2319676	0.83[JPT][hapmap]
rs2319677	0.88[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2477106	0.81[ASW][hapmap];0.87[JPT][hapmap]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.81[JPT][hapmap]
rs2477114	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2477117	0.81[ASW][hapmap]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.86[JPT][hapmap]
rs2483622	0.87[JPT][hapmap]
rs2501608	0.87[JPT][hapmap]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501615	0.81[JPT][hapmap]
rs2501621	0.87[JPT][hapmap]
rs2762859	0.81[JPT][hapmap]
rs2777910	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2985373	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147170	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs4147171	0.82[EUR][1000 genomes]
rs4379644	0.81[ASW][hapmap]
rs4622030	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs4652461	0.80[ASW][hapmap]
rs4652470	0.82[CHD][hapmap]
rs483307	0.81[JPT][hapmap]
rs500371	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs504202	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs510209	0.81[JPT][hapmap]
rs511332	0.92[ASN][1000 genomes]
rs521858	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs526683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs528350	0.93[JPT][hapmap]
rs533795	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs534168	0.93[JPT][hapmap]
rs539324	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552743	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs552763	0.85[ASN][1000 genomes]
rs561233	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs585355	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6425606	0.89[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs6425607	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs6676989	0.81[ASW][hapmap]
rs6682558	0.89[ASW][hapmap];0.87[CEU][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs7521895	1.00[JPT][hapmap]
rs7521948	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs551607	CEP350	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179899600-179905000	Weak transcription	GM12878-XiMat	blood
2	chr1:179902000-179907800	Weak transcription	Stomach Mucosa	stomach
3	chr1:179902200-179906800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links