Variant report

Variant	rs4974147
Chromosome Location	chr3:55859367-55859368
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	chr3:55850876..55853376-chr3:55857822..55860534,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1495365	0.82[CHB][hapmap]
rs1495366	0.82[CHB][hapmap]
rs17714443	0.82[ASN][1000 genomes]
rs4129823	0.80[ASN][1000 genomes]
rs4459870	0.87[ASN][1000 genomes]
rs4955877	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs4955878	0.81[CEU][hapmap]
rs4955882	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4955884	0.84[ASN][1000 genomes]
rs4974113	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7615473	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9815001	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835091	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9840522	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9852746	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9852888	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9853067	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854025	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854247	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9857120	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9860951	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9874792	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv590361	chr3:55834871-55876104	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4974147	HESX1	cis	cerebellum	SCAN
rs4974147	TWF2	cis	parietal	SCAN
rs4974147	CCDC66	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55847600-55860200	Weak transcription	Fetal Lung	lung
2	chr3:55858800-55860000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links