Variant report

Variant	rs1117254
Chromosome Location	chr7:117797066-117797067
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: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10085904	0.89[EUR][1000 genomes]
rs10226152	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10227326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10229589	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10241875	0.85[EUR][1000 genomes]
rs10252627	0.85[EUR][1000 genomes]
rs10267938	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10487390	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1054032	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1061731	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953864	0.90[EUR][1000 genomes]
rs11486992	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11543742	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11770353	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979012	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12112697	0.82[EUR][1000 genomes]
rs12537795	0.90[EUR][1000 genomes]
rs12667103	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13224733	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2058417	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2191920	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402322	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896242	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802012	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141028	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41900	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41901	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41902	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41905	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41906	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41909	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41910	0.87[EUR][1000 genomes]
rs41911	0.87[EUR][1000 genomes]
rs41915	0.86[EUR][1000 genomes]
rs41916	0.86[EUR][1000 genomes]
rs41926	0.86[EUR][1000 genomes]
rs41933	0.85[EUR][1000 genomes]
rs41934	0.87[EUR][1000 genomes]
rs41935	0.87[EUR][1000 genomes]
rs41938	0.87[EUR][1000 genomes]
rs41939	0.87[EUR][1000 genomes]
rs41960	0.81[EUR][1000 genomes]
rs5002233	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6466650	0.81[EUR][1000 genomes]
rs6944524	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6946855	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6948096	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956486	0.90[EUR][1000 genomes]
rs6964911	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6965144	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7779933	0.89[EUR][1000 genomes]
rs7796145	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7796148	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7797855	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7799229	0.88[EUR][1000 genomes]
rs7806490	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917761	0.87[EUR][1000 genomes]
rs9655829	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9656260	0.90[EUR][1000 genomes]
rs979652	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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
rs1117254	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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