Variant report

Variant	rs1311911
Chromosome Location	chr6:28705074-28705075
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28705003..28707799-chr6:28889865..28891695,2	K562	blood:
2	chr6:28694465..28699409-chr6:28701823..28706376,12	K562	blood:
3	chr6:28702781..28705852-chr6:28730775..28732422,3	K562	blood:
4	chr6:28704284..28707045-chr6:28723983..28725942,2	MCF-7	breast:
5	chr6:28687230..28688788-chr6:28703405..28705827,2	K562	blood:
6	chr6:28704393..28708100-chr6:28724005..28727294,4	K562	blood:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1233579	0.98[EUR][1000 genomes]
rs1233580	0.98[EUR][1000 genomes]
rs1233581	0.98[EUR][1000 genomes]
rs1233583	0.98[EUR][1000 genomes]
rs1233593	0.98[EUR][1000 genomes]
rs1233594	0.98[EUR][1000 genomes]
rs1233599	0.94[EUR][1000 genomes]
rs1233600	0.94[EUR][1000 genomes]
rs1233604	0.94[EUR][1000 genomes]
rs1233618	0.94[EUR][1000 genomes]
rs1233620	0.94[EUR][1000 genomes]
rs1233623	0.94[EUR][1000 genomes]
rs1238262	0.98[EUR][1000 genomes]
rs1311912	0.98[EUR][1000 genomes]
rs1311913	0.98[EUR][1000 genomes]
rs13194504	0.85[EUR][1000 genomes]
rs13217472	0.91[EUR][1000 genomes]
rs1742743	0.96[EUR][1000 genomes]
rs3131340	0.82[EUR][1000 genomes]
rs3131341	0.82[EUR][1000 genomes]
rs3131343	0.84[EUR][1000 genomes]
rs3132373	0.84[EUR][1000 genomes]
rs3132396	0.82[EUR][1000 genomes]
rs3135294	0.80[EUR][1000 genomes]
rs34724414	0.85[EUR][1000 genomes]
rs35044849	0.85[EUR][1000 genomes]
rs35243068	0.91[EUR][1000 genomes]
rs4324798	0.82[EUR][1000 genomes]
rs6456835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6908726	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7761321	0.84[EUR][1000 genomes]
rs7764642	0.93[EUR][1000 genomes]
rs7766699	0.81[EUR][1000 genomes]
rs7767099	0.84[EUR][1000 genomes]
rs9257133	0.98[EUR][1000 genomes]
rs9257136	0.98[EUR][1000 genomes]
rs9257137	0.98[EUR][1000 genomes]
rs9257140	0.98[EUR][1000 genomes]
rs9257167	0.94[EUR][1000 genomes]
rs9257183	0.94[EUR][1000 genomes]
rs9257184	0.94[EUR][1000 genomes]
rs9257187	0.94[EUR][1000 genomes]
rs9257188	0.94[EUR][1000 genomes]
rs9257189	0.94[EUR][1000 genomes]
rs9257192	0.94[EUR][1000 genomes]
rs9257217	0.84[EUR][1000 genomes]
rs9257223	0.82[EUR][1000 genomes]
rs9393926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9393929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1311911	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1311911	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1311911	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28702200-28705600	Active TSS	A549	lung
2	chr6:28703000-28705200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:28703800-28705400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28704400-28705200	Weak transcription	K562	blood
5	chr6:28704400-28705800	Weak transcription	HMEC	breast
6	chr6:28704600-28705400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28705000-28707200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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