Variant report

Variant	rs6689375
Chromosome Location	chr1:227721627-227721628
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227721387..227723792-chr1:227750003..227751668,2	MCF-7	breast:
2	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
3	chr1:227699513..227702199-chr1:227720616..227723558,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1045407	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753436	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753437	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799422	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799424	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799428	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799437	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799444	0.82[EUR][1000 genomes]
rs10916154	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916157	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916160	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916161	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916162	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916163	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916166	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916167	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916173	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916180	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916189	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916199	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11576992	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11581704	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590390	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058246	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081818	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12084072	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12092054	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093031	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116848	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119889	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120182	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123996	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129704	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12129894	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131114	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12133625	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138198	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138229	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140813	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140848	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390401	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1495848	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1845757	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1995019	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2172936	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28446171	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999742	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34421331	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3942992	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4379651	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57158394	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61824940	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426470	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426471	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426472	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656661	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659012	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659349	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669236	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669277	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672530	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678802	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679855	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691443	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692376	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694427	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696239	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698409	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74140304	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7418348	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521812	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531801	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538206	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7538893	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540382	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549475	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551788	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553531	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903691	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951084	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726691	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv945338	chr1:227712483-227722545	ZNF genes & repeats Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6689375	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227714200-227721800	ZNF genes & repeats	Liver	Liver
2	chr1:227718600-227723200	Weak transcription	Psoas Muscle	Psoas
3	chr1:227720000-227722000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:227720800-227725800	Weak transcription	Pancreas	Pancrea
5	chr1:227720800-227729200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:227720800-227729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:227721200-227725800	Weak transcription	Aorta	Aorta

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