Variant report

Variant	rs12084072
Chromosome Location	chr1:227727584-227727585
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
2	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
3	chr1:227725139..227726773-chr1:227727190..227729662,2	K562	blood:
4	chr1:227726703..227728573-chr1:227729012..227731358,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1045407	0.84[EUR][1000 genomes]
rs10753436	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10753437	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10799422	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799424	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799428	0.88[EUR][1000 genomes]
rs10799437	0.84[EUR][1000 genomes]
rs10916154	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916157	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916160	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916161	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916162	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916163	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916166	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916167	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916173	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10916180	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916189	0.84[EUR][1000 genomes]
rs11581704	0.84[EUR][1000 genomes]
rs11590390	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12081818	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12092054	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12093031	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12116848	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12119889	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12120182	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12123996	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12129704	0.83[EUR][1000 genomes]
rs12129894	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12131114	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133625	0.84[EUR][1000 genomes]
rs12140813	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12140848	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1390401	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1495848	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1995019	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2172936	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28446171	0.83[EUR][1000 genomes]
rs2999742	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3942992	0.85[EUR][1000 genomes]
rs4379651	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57158394	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61824940	0.83[EUR][1000 genomes]
rs6426470	0.82[EUR][1000 genomes]
rs6426471	0.82[EUR][1000 genomes]
rs6426472	0.81[EUR][1000 genomes]
rs6656661	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6659012	0.84[EUR][1000 genomes]
rs6659349	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669236	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669277	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672530	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6678802	0.84[EUR][1000 genomes]
rs6679855	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6689375	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6691443	0.82[EUR][1000 genomes]
rs6692376	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6694427	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6696239	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6698409	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74140304	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7418348	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7521812	0.84[EUR][1000 genomes]
rs7538206	0.80[EUR][1000 genomes]
rs7538893	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7540382	0.80[EUR][1000 genomes]
rs7549475	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7551788	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7553531	0.81[EUR][1000 genomes]
rs903691	0.89[EUR][1000 genomes]
rs951084	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9726691	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12084072	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227720800-227729200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:227720800-227729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:227725200-227729000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227726200-227728600	Weak transcription	Pancreas	Pancrea
5	chr1:227726200-227729600	Weak transcription	Aorta	Aorta
6	chr1:227726400-227729200	Weak transcription	Liver	Liver

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