Variant report

Variant	rs62466515
Chromosome Location	chr7:117841157-117841158
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:117819950..117822921-chr7:117839591..117842038,2	MCF-7	breast:
2	chr7:117838537..117840659-chr7:117840686..117843099,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1015782	0.86[EUR][1000 genomes]
rs10247768	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10487392	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11487110	0.86[EUR][1000 genomes]
rs11542074	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11974039	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11983651	0.91[EUR][1000 genomes]
rs12154684	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670769	0.83[EUR][1000 genomes]
rs1544583	0.94[EUR][1000 genomes]
rs1544584	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17140984	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17141053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2058418	0.84[EUR][1000 genomes]
rs2215628	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286863	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28260	0.83[EUR][1000 genomes]
rs33924981	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34010516	0.94[EUR][1000 genomes]
rs34019303	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35218902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35485182	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41903	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41904	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41912	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41921	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41923	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41924	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41925	0.83[EUR][1000 genomes]
rs41930	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41931	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41936	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41962	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41989	0.82[EUR][1000 genomes]
rs45604739	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4730837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5002232	0.84[EUR][1000 genomes]
rs57308869	0.83[ASN][1000 genomes]
rs61328879	0.82[EUR][1000 genomes]
rs62466471	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468297	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62469806	0.90[EUR][1000 genomes]
rs6466643	0.82[EUR][1000 genomes]
rs6466648	0.86[EUR][1000 genomes]
rs6942513	0.82[EUR][1000 genomes]
rs6972105	0.80[EUR][1000 genomes]
rs769435	0.82[EUR][1000 genomes]
rs7786233	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7801976	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9641593	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9656259	0.86[EUR][1000 genomes]
rs992035	0.82[EUR][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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466515	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
2	chr7:117825800-117842600	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:117830400-117842400	Weak transcription	Fetal Lung	lung
4	chr7:117831200-117842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:117832800-117842200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:117833000-117854000	Weak transcription	HSMM	muscle
7	chr7:117833400-117842200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:117833600-117854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:117834000-117842000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:117834400-117843400	Weak transcription	Fetal Thymus	thymus
11	chr7:117839400-117843600	Weak transcription	Primary B cells from cord blood	blood

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