Variant report

No.	Distal block	Cell Line	Cell type
1	chr6:28665079..28666654-chr6:28669944..28671678,2	K562	blood:
2	chr6:28664889..28672891-chr6:28674189..28678694,12	K562	blood:
3	chr6:28670960..28673190-chr6:28724668..28726201,2	K562	blood:

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1233579	0.91[EUR][1000 genomes]
rs1233580	0.91[EUR][1000 genomes]
rs1233581	0.91[EUR][1000 genomes]
rs1233583	0.91[EUR][1000 genomes]
rs1233593	0.91[EUR][1000 genomes]
rs1233594	0.91[EUR][1000 genomes]
rs1233599	0.87[EUR][1000 genomes]
rs1233600	0.87[EUR][1000 genomes]
rs1233604	0.87[EUR][1000 genomes]
rs1233618	0.87[EUR][1000 genomes]
rs1233620	0.87[EUR][1000 genomes]
rs1233623	0.87[EUR][1000 genomes]
rs1238262	0.91[EUR][1000 genomes]
rs1311911	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1311912	0.91[EUR][1000 genomes]
rs1311913	0.91[EUR][1000 genomes]
rs13194504	0.93[EUR][1000 genomes]
rs13217472	0.98[EUR][1000 genomes]
rs1742743	0.89[EUR][1000 genomes]
rs34724414	0.93[EUR][1000 genomes]
rs35044849	0.93[EUR][1000 genomes]
rs35243068	0.98[EUR][1000 genomes]
rs6456835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7764642	0.86[EUR][1000 genomes]
rs9257133	0.91[EUR][1000 genomes]
rs9257136	0.91[EUR][1000 genomes]
rs9257137	0.91[EUR][1000 genomes]
rs9257140	0.91[EUR][1000 genomes]
rs9257167	0.87[EUR][1000 genomes]
rs9257183	0.87[EUR][1000 genomes]
rs9257184	0.87[EUR][1000 genomes]
rs9257187	0.87[EUR][1000 genomes]
rs9257188	0.87[EUR][1000 genomes]
rs9257189	0.87[EUR][1000 genomes]
rs9257192	0.87[EUR][1000 genomes]
rs9393925	0.83[EUR][1000 genomes]
rs9393926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9393929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6908726	HLA-H	cis	multi-tissue	Pritchard
rs6908726	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6908726	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs6908726	HLA-A	cis	multi-tissue	Pritchard
rs6908726	HLA-G	cis	multi-tissue	Pritchard
rs6908726	ZFP57	cis	multi-tissue	Pritchard
rs6908726	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6908726	HLA-DRB1	cis	multi-tissue	Pritchard
rs6908726	BTN3A2	cis	multi-tissue	Pritchard
rs6908726	ZNF323	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28668600-28676400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:28671000-28671600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:28671200-28671800	Strong transcription	K562	blood

Quick Search: