Variant report

Variant	rs1742743
Chromosome Location	chr6:28724082-28724083
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
2	chr6:28723357..28725477-chr6:28861527..28864312,2	K562	blood:
3	chr6:28723896..28728359-chr6:28734827..28738855,4	K562	blood:
4	chr6:28704393..28708100-chr6:28724005..28727294,4	K562	blood:
5	chr6:28722382..28725655-chr6:28783034..28786428,3	K562	blood:
6	chr6:28721787..28724398-chr9:131939083..131940744,2	MCF-7	breast:
7	chr6:28706832..28708574-chr6:28723413..28725632,2	K562	blood:
8	chr6:28704284..28707045-chr6:28723983..28725942,2	MCF-7	breast:
9	chr6:28723977..28727923-chr6:28779903..28783132,3	K562	blood:
10	chr6:28723896..28728359-chr6:28734827..28738855,6	K562	blood:
11	chr6:28723907..28726622-chr6:28947645..28950512,2	K562	blood:
12	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:
13	chr6:28722382..28724843-chr6:28784005..28786428,2	K562	blood:
14	chr6:28652217..28653747-chr6:28722642..28724791,2	K562	blood:
15	chr6:28712043..28717130-chr6:28723838..28729658,8	K562	blood:
16	chr6:28723125..28726078-chr6:28775767..28777359,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188483	Chromatin interaction
ENSG00000224157	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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233581	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1238262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1311911	0.96[EUR][1000 genomes]
rs1311912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1311913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13194504	0.85[EUR][1000 genomes]
rs13217472	0.91[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	0.93[EUR][1000 genomes]
rs6908726	0.89[EUR][1000 genomes]
rs7761321	0.84[EUR][1000 genomes]
rs7764642	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7766699	0.80[EUR][1000 genomes]
rs7767099	0.84[EUR][1000 genomes]
rs9257133	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257136	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257140	0.98[EUR][1000 genomes]
rs9257167	0.94[EUR][1000 genomes]
rs9257183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257184	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257187	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257188	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257189	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257192	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257217	0.84[EUR][1000 genomes]
rs9257223	0.82[EUR][1000 genomes]
rs9393926	0.89[EUR][1000 genomes]
rs9393929	0.86[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
rs1742743	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1742743	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1742743	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28715400-28725000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:28715600-28724800	Weak transcription	HMEC	breast
3	chr6:28718800-28724600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:28723800-28724200	Enhancers	A549	lung
5	chr6:28723800-28724400	Bivalent Enhancer	HepG2	liver
6	chr6:28724000-28724200	Flanking Active TSS	Placenta	Placenta
7	chr6:28724000-28724200	Active TSS	K562	blood
8	chr6:28724000-28726400	Active TSS	Hela-S3	cervix

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