Variant report

Variant	rs477485
Chromosome Location	chr1:215095527-215095528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215094543..215096510-chr1:215106179..215108957,2	K562	blood:
2	chr1:215038350..215040423-chr1:215095466..215098251,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11120449	0.88[ASN][1000 genomes]
rs1377185	0.87[ASN][1000 genomes]
rs472961	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475341	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs476910	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478664	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs486980	0.82[ASN][1000 genomes]
rs487527	0.81[ASN][1000 genomes]
rs494808	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs497870	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap]
rs501475	0.92[ASN][1000 genomes]
rs506436	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506765	0.92[ASN][1000 genomes]
rs512597	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520394	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs520982	0.92[ASN][1000 genomes]
rs526746	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs527388	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527769	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530931	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap]
rs534411	0.92[ASN][1000 genomes]
rs542158	0.82[ASN][1000 genomes]
rs549523	0.81[ASN][1000 genomes]
rs554343	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556648	0.81[ASN][1000 genomes]
rs557765	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs558728	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs558879	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs559944	0.88[ASN][1000 genomes]
rs561766	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs562935	0.92[ASN][1000 genomes]
rs564291	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566170	0.89[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs6540867	0.88[YRI][hapmap]
rs6658958	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6684902	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6690944	0.88[ASN][1000 genomes]
rs896652	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv873167	chr1:214950361-215116947	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs477485	C1orf227	cis	parietal	SCAN
rs477485	LEF1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215085800-215097800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:215092800-215096400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:215094400-215095600	Enhancers	HMEC	breast

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