Variant report

Variant	rs12906134
Chromosome Location	chr15:49969620-49969621
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49968518..49970892-chr15:49980860..49984000,3	MCF-7	breast:
2	chr15:49968339..49970198-chr15:49970893..49972415,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10851479	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070695	0.83[ASN][1000 genomes]
rs11634947	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11637582	0.96[ASN][1000 genomes]
rs11852336	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853248	0.88[ASN][1000 genomes]
rs11854671	0.87[ASN][1000 genomes]
rs11858411	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12050614	0.92[ASN][1000 genomes]
rs12050624	0.96[ASN][1000 genomes]
rs12148764	0.90[ASN][1000 genomes]
rs12232355	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12591317	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591659	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593151	0.90[ASN][1000 genomes]
rs12595692	0.90[ASN][1000 genomes]
rs12901680	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902960	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906972	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907661	0.86[ASN][1000 genomes]
rs12907918	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12907944	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908624	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908635	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912703	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1395901	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395903	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17404727	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17479589	0.90[ASN][1000 genomes]
rs1911612	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1948975	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976551	0.86[ASN][1000 genomes]
rs2413956	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899434	0.90[ASN][1000 genomes]
rs34002493	0.90[ASN][1000 genomes]
rs34146550	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34246470	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34414487	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34694913	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34941109	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35698479	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4436732	0.90[ASN][1000 genomes]
rs4480740	0.90[ASN][1000 genomes]
rs4547278	0.90[ASN][1000 genomes]
rs4775816	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55904469	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62009977	0.90[ASN][1000 genomes]
rs62021589	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022665	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022667	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022700	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493372	0.90[ASN][1000 genomes]
rs7162741	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172906	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174135	0.90[ASN][1000 genomes]
rs7180421	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8032688	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033476	0.96[ASN][1000 genomes]
rs925104	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12906134	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49966800-49970000	Weak transcription	Ovary	ovary
2	chr15:49966800-49987400	Weak transcription	NHLF	lung
3	chr15:49968000-49969800	Weak transcription	Hela-S3	cervix
4	chr15:49968200-49971000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:49968400-49970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:49968600-49971000	Weak transcription	NHDF-Ad	bronchial

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