Variant report

Variant	rs1264709
Chromosome Location	chr6:30056476-30056477
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1264705	0.93[AFR][1000 genomes]
rs1264706	0.93[AFR][1000 genomes]
rs1632926	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508036	0.81[ASN][1000 genomes]
rs2524005	0.85[CEU][hapmap]
rs259926	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780084	0.91[ASN][1000 genomes]
rs28780085	0.91[ASN][1000 genomes]
rs3129012	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356959	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356971	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369073	1.00[ASN][1000 genomes]
rs9260628	0.81[ASN][1000 genomes]
rs9260629	0.81[ASN][1000 genomes]
rs9261259	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1264709	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1264709	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs1264709	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1264709	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1264709	Hs.519979	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30048000-30058400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:30055600-30059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:30056400-30059200	Weak transcription	NHEK	skin
4	chr6:30056400-30059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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