Variant report

Variant	rs28539674
Chromosome Location	chr15:41409821-41409822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41407384-41409854	K562	blood:	n/a	n/a
2	POLR2A	chr15:41407967-41409937	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:41409349..41412007-chr15:41415767..41418132,2	K562	blood:
2	chr15:41409067..41410859-chr15:41519821..41522050,2	K562	blood:
3	chr15:41408589..41410514-chr15:41411764..41413271,2	K562	blood:
4	chr15:41407604..41409854-chr15:41574990..41577590,2	K562	blood:
5	chr15:41220723..41224054-chr15:41407218..41409948,5	K562	blood:
6	chr15:41408234..41410047-chr15:41521744..41524372,2	MCF-7	breast:
7	chr15:41198680..41200257-chr15:41407183..41410024,3	MCF-7	breast:

No data

Variant related genes	Relation type
INO80	TF binding region
ENSG00000247556	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000178997	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11858278	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551767	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28896021	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv3355696	chr15:41407285-41409833	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28539674	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28539674	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28539674	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28539674	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41409600-41414800	Weak transcription	HepG2	liver
2	chr15:41409600-41417400	Weak transcription	A549	lung
3	chr15:41409600-41427600	Weak transcription	Hela-S3	cervix

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