Variant report

Variant	rs12154684
Chromosome Location	chr7:117799391-117799392
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	chr7:117799378..117801536-chr7:117822814..117824466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128534	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1015782	0.83[EUR][1000 genomes]
rs10247768	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10487392	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11487110	0.83[EUR][1000 genomes]
rs11542074	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11974039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11983651	0.84[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1544583	0.92[EUR][1000 genomes]
rs1544584	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17140984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17141053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058418	0.81[EUR][1000 genomes]
rs2215628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286863	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28260	0.80[EUR][1000 genomes]
rs33924981	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34010516	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34019303	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35218902	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35485182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41903	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41904	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41912	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41921	0.83[EUR][1000 genomes]
rs41923	0.84[EUR][1000 genomes]
rs41924	0.84[EUR][1000 genomes]
rs41925	0.80[EUR][1000 genomes]
rs41930	0.84[EUR][1000 genomes]
rs41931	0.86[EUR][1000 genomes]
rs41936	0.85[EUR][1000 genomes]
rs41962	0.81[EUR][1000 genomes]
rs41989	0.81[EUR][1000 genomes]
rs4535672	0.80[EUR][1000 genomes]
rs45604739	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4730837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5002232	0.82[EUR][1000 genomes]
rs57308869	0.83[ASN][1000 genomes]
rs62466471	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62466515	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62468297	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62469806	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6466643	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6466648	0.83[EUR][1000 genomes]
rs6972105	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7786233	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7801976	0.84[EUR][1000 genomes]
rs9641593	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9656259	0.83[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
rs12154684	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117791200-117815800	Weak transcription	Psoas Muscle	Psoas

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