Variant report

Variant	rs62485452
Chromosome Location	chr7:140675159-140675160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140675007..140675968-chr7:140692355..140692975,3	MCF-7	breast:
2	chr7:140675000..140676654-chr7:140692083..140692972,8	MCF-7	breast:
3	chr7:140667563..140669142-chr7:140674491..140677083,2	MCF-7	breast:
4	chr7:140674937..140676218-chr7:140692083..140692979,12	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10240888	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255167	0.91[ASN][1000 genomes]
rs10265001	0.84[ASN][1000 genomes]
rs10268118	0.86[ASN][1000 genomes]
rs10281975	0.80[EUR][1000 genomes]
rs1044927	0.82[ASN][1000 genomes]
rs10488098	0.84[EUR][1000 genomes]
rs1089264	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10952364	0.87[ASN][1000 genomes]
rs12538296	0.89[ASN][1000 genomes]
rs13236223	0.84[ASN][1000 genomes]
rs13438418	0.80[EUR][1000 genomes]
rs13438609	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476868	0.84[EUR][1000 genomes]
rs16882367	0.84[ASN][1000 genomes]
rs17622717	0.84[EUR][1000 genomes]
rs17623204	0.84[EUR][1000 genomes]
rs17695341	0.84[EUR][1000 genomes]
rs17695623	0.84[EUR][1000 genomes]
rs17695707	0.82[EUR][1000 genomes]
rs17695995	0.84[EUR][1000 genomes]
rs2079827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688430	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3852286	0.86[ASN][1000 genomes]
rs3864527	0.86[ASN][1000 genomes]
rs38715	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38717	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38718	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38719	0.93[EUR][1000 genomes]
rs38720	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38722	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38723	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38726	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38730	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38731	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38734	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38736	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38739	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38740	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55720380	0.84[EUR][1000 genomes]
rs55875248	0.84[EUR][1000 genomes]
rs56347011	0.88[EUR][1000 genomes]
rs57143942	0.80[EUR][1000 genomes]
rs57675404	0.84[EUR][1000 genomes]
rs57846481	0.84[EUR][1000 genomes]
rs58901822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59183598	0.84[EUR][1000 genomes]
rs59232128	0.84[EUR][1000 genomes]
rs59477283	0.84[EUR][1000 genomes]
rs59816436	0.84[EUR][1000 genomes]
rs60081231	0.84[EUR][1000 genomes]
rs60164573	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60251368	0.84[EUR][1000 genomes]
rs62484288	0.84[EUR][1000 genomes]
rs62484291	0.84[EUR][1000 genomes]
rs62484294	0.84[EUR][1000 genomes]
rs62484295	0.82[EUR][1000 genomes]
rs62484299	0.84[EUR][1000 genomes]
rs62484300	0.84[EUR][1000 genomes]
rs62485366	0.84[EUR][1000 genomes]
rs62485368	0.84[EUR][1000 genomes]
rs62485369	0.80[EUR][1000 genomes]
rs62485370	0.84[EUR][1000 genomes]
rs62485372	0.84[EUR][1000 genomes]
rs62485377	0.82[EUR][1000 genomes]
rs62485379	0.82[EUR][1000 genomes]
rs62485383	0.84[EUR][1000 genomes]
rs62485390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62485391	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62485451	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62485453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6464217	0.89[ASN][1000 genomes]
rs6662	0.82[ASN][1000 genomes]
rs6971577	0.82[ASN][1000 genomes]
rs7810757	0.80[EUR][1000 genomes]
rs801117	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs801121	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs801127	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1797438	chr7:140666808-140682332	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv520944	chr7:140673779-140679684	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62485452	MRPS33	Cis_1M	lymphoblastoid	RTeQTL
rs62485452	BRAF	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140673800-140675400	Weak transcription	Fetal Intestine Large	intestine
2	chr7:140673800-140675600	Weak transcription	Liver	Liver
3	chr7:140673800-140675600	Weak transcription	Placenta	Placenta
4	chr7:140674000-140675400	Weak transcription	Adipose Nuclei	Adipose
5	chr7:140674000-140675400	Weak transcription	Fetal Intestine Small	intestine
6	chr7:140674000-140675800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:140674800-140675400	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links