Variant report

Variant	rs7957839
Chromosome Location	chr12:123941055-123941056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123919731..123922838-chr12:123939726..123943639,4	MCF-7	breast:
2	chr12:123940979..123946241-chr12:123948686..123953480,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150977	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11497310	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11507743	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11516174	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11516175	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11516178	0.88[EUR][1000 genomes]
rs11522341	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11522342	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11522343	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11523309	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11535679	0.97[EUR][1000 genomes]
rs13303358	0.87[EUR][1000 genomes]
rs28493578	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28703907	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28728075	0.87[EUR][1000 genomes]
rs28781570	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894691	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61953496	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9697330	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9697415	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9697423	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9723026	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9723244	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9777715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9777830	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7957839	DDX55	cis	cerebellum	SCAN
rs7957839	ANAPC5	cis	parietal	SCAN
rs7957839	UNC119B	cis	cerebellum	SCAN
rs7957839	TMED3	trans	parietal	SCAN
rs7957839	TCTN2	cis	cerebellum	SCAN
rs7957839	DDX55	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123933400-123942200	Weak transcription	Thymus	Thymus
2	chr12:123934200-123942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:123937200-123942200	Weak transcription	Placenta	Placenta
4	chr12:123938200-123942400	Weak transcription	HepG2	liver
5	chr12:123939800-123942400	Weak transcription	K562	blood

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