Variant report

Variant	rs59112029
Chromosome Location	chr15:49942288-49942289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:49942142-49943574	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr15:49942243-49942570	HepG2	liver:	n/a	n/a
3	JUN	chr15:49942228-49942396	K562	blood:	n/a	n/a
4	POLR2A	chr15:49941948-49942727	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49928185..49930048-chr15:49941655..49944211,2	K562	blood:
2	chr15:49911752..49916656-chr15:49939453..49943978,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261597	TF binding region
ENSG00000166262	Chromatin interaction
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10220770	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10220846	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10519234	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10519235	0.81[AMR][1000 genomes]
rs10519238	0.90[AMR][1000 genomes]
rs1055135	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13313447	0.81[AMR][1000 genomes]
rs16962663	0.81[AMR][1000 genomes]
rs16962664	0.81[AMR][1000 genomes]
rs16962666	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16962668	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16962670	0.81[AMR][1000 genomes]
rs16962676	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16962680	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16962697	0.81[AMR][1000 genomes]
rs16962735	0.90[AMR][1000 genomes]
rs1911618	1.00[AMR][1000 genomes]
rs58889385	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59565793	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59749619	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59942223	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60640257	0.90[AMR][1000 genomes]
rs7175199	0.81[AFR][1000 genomes]
rs7175805	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7176887	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73391021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73391038	0.90[AMR][1000 genomes]
rs73391046	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406036	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406046	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406051	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406052	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406056	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406060	0.90[AMR][1000 genomes]
rs73406069	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406085	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73406091	0.81[AMR][1000 genomes]
rs73406098	0.81[AMR][1000 genomes]
rs73406100	0.81[AMR][1000 genomes]
rs73407903	0.81[AMR][1000 genomes]
rs73407904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407908	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012439	0.81[AMR][1000 genomes]
rs74012441	0.81[AMR][1000 genomes]
rs8039808	0.90[AMR][1000 genomes]
rs8041629	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8041771	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9652425	0.99[AFR][1000 genomes];1.00[AMR][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	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49928200-49943000	Weak transcription	Lung	lung
2	chr15:49938400-49944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:49938400-49944600	Weak transcription	Ovary	ovary
4	chr15:49938400-49945400	Weak transcription	Fetal Heart	heart
5	chr15:49938800-49946200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:49939000-49943200	Weak transcription	Aorta	Aorta
7	chr15:49939000-49944400	Weak transcription	HSMMtube	muscle
8	chr15:49939000-49944600	Weak transcription	Osteobl	bone
9	chr15:49939000-49945000	Weak transcription	Left Ventricle	heart
10	chr15:49939800-49942400	Weak transcription	NHDF-Ad	bronchial
11	chr15:49939800-49942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:49939800-49942800	Weak transcription	HSMM	muscle
13	chr15:49940000-49944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:49942200-49942400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr15:49942200-49942600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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