Variant report

Variant	rs11974039
Chromosome Location	chr7:117797816-117797817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:117792959..117795315-chr7:117796416..117799044,2	MCF-7	breast:
2	chr7:117796437..117798170-chr7:117822547..117825191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128534	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1015782	0.80[EUR][1000 genomes]
rs10247768	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10487392	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11487110	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs11542074	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11983651	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12154684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544583	0.89[EUR][1000 genomes]
rs1544584	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17140984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17141053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041527	0.81[CEU][hapmap]
rs2058418	0.88[CEU][hapmap]
rs2215628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286863	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs33924981	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34010516	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34019303	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35218902	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35485182	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41903	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41904	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41912	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41921	0.81[EUR][1000 genomes]
rs41923	0.82[EUR][1000 genomes]
rs41924	0.82[EUR][1000 genomes]
rs41930	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41931	0.84[EUR][1000 genomes]
rs41936	0.83[EUR][1000 genomes]
rs45604739	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57308869	0.81[ASN][1000 genomes]
rs62466471	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466515	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62468297	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62469806	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6466643	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6466648	0.80[EUR][1000 genomes]
rs6942513	0.81[CEU][hapmap]
rs6972105	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs769435	0.84[CEU][hapmap]
rs7786233	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801976	0.82[EUR][1000 genomes]
rs9641593	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656259	0.80[EUR][1000 genomes]
rs992035	0.84[CEU][hapmap]

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
rs11974039	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117791200-117815800	Weak transcription	Psoas Muscle	Psoas
2	chr7:117793200-117798000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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