Variant report

Variant	rs1354469
Chromosome Location	chr12:60668356-60668357
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	chr12:60659638..60662506-chr12:60667723..60669431,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1021887	0.80[EUR][1000 genomes]
rs10747870	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784028	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10784029	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10784033	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784046	0.80[EUR][1000 genomes]
rs10877398	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877399	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877401	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877402	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877403	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877406	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877412	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877413	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877414	0.88[EUR][1000 genomes]
rs11173338	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11173357	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173365	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173371	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11173386	0.87[EUR][1000 genomes]
rs11173387	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173389	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11173391	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11173392	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11173393	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11173395	0.88[EUR][1000 genomes]
rs11173397	0.88[EUR][1000 genomes]
rs11173398	0.88[EUR][1000 genomes]
rs11561446	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11561447	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11836206	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12228823	0.85[EUR][1000 genomes]
rs12230599	0.86[EUR][1000 genomes]
rs12817959	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12830074	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1304313	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319775	0.83[EUR][1000 genomes]
rs1389255	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1389256	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1493311	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493318	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1504442	0.87[EUR][1000 genomes]
rs1504443	0.87[EUR][1000 genomes]
rs1504444	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1587821	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1604866	0.80[EUR][1000 genomes]
rs1910674	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1995515	0.90[EUR][1000 genomes]
rs2014074	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2134882	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202365	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2221407	0.88[EUR][1000 genomes]
rs2363600	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35713358	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3847662	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3847663	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3907482	0.87[AMR][1000 genomes]
rs3920119	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4093759	0.85[AMR][1000 genomes]
rs4143650	0.81[EUR][1000 genomes]
rs4254103	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4265627	0.81[EUR][1000 genomes]
rs4347425	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4366523	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4406858	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4625509	0.81[AMR][1000 genomes]
rs4758855	0.82[AMR][1000 genomes]
rs4758858	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758859	0.87[EUR][1000 genomes]
rs56240683	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60691341	0.88[EUR][1000 genomes]
rs61487567	0.86[EUR][1000 genomes]
rs61923092	0.81[EUR][1000 genomes]
rs61923093	0.82[EUR][1000 genomes]
rs61923121	0.83[EUR][1000 genomes]
rs61923124	0.87[EUR][1000 genomes]
rs61923127	0.87[EUR][1000 genomes]
rs61923129	0.87[EUR][1000 genomes]
rs61923130	0.86[EUR][1000 genomes]
rs61923132	0.86[EUR][1000 genomes]
rs61923155	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581305	0.81[EUR][1000 genomes]
rs6581310	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7134267	0.85[EUR][1000 genomes]
rs7134663	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7136435	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136994	0.86[EUR][1000 genomes]
rs7138626	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7138854	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295183	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7297548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298315	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7300532	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7305978	0.81[EUR][1000 genomes]
rs7306226	0.87[EUR][1000 genomes]
rs7312225	0.92[EUR][1000 genomes]
rs7313364	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952971	0.88[EUR][1000 genomes]
rs7953857	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7957100	0.84[EUR][1000 genomes]
rs7957295	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7960292	0.87[EUR][1000 genomes]
rs7960303	0.87[EUR][1000 genomes]
rs7960487	0.87[EUR][1000 genomes]
rs7961221	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961816	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967860	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7973156	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975549	0.81[EUR][1000 genomes]
rs7977065	0.85[AMR][1000 genomes]
rs924836	0.88[EUR][1000 genomes]
rs958543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959645	0.82[EUR][1000 genomes]
rs9634280	0.87[EUR][1000 genomes]
rs9634281	0.87[EUR][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	nsv899137	chr12:60568891-60797083	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1054287	chr12:60601870-60861866	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv832431	chr12:60626292-60809233	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1354469	KIAA1143	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60663800-60675600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:60664200-60675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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