Variant report

Variant	rs6042298
Chromosome Location	chr20:13652862-13652863
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13652495..13656691-chr20:13764074..13766067,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101247	Chromatin interaction
ENSG00000089048	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13433337	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033774	1.00[AMR][1000 genomes]
rs6033782	1.00[AMR][1000 genomes]
rs6033784	1.00[AMR][1000 genomes]
rs6033791	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033797	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042246	1.00[AMR][1000 genomes]
rs6042247	1.00[AMR][1000 genomes]
rs6042248	1.00[AMR][1000 genomes]
rs6042249	1.00[AMR][1000 genomes]
rs6042252	1.00[AMR][1000 genomes]
rs6042265	1.00[AMR][1000 genomes]
rs6042267	1.00[AMR][1000 genomes]
rs6042286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6105145	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109972	1.00[AMR][1000 genomes]
rs6109973	1.00[AMR][1000 genomes]
rs6109985	1.00[AMR][1000 genomes]
rs6109996	0.84[AFR][1000 genomes]
rs73270770	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13649400-13653600	Enhancers	Dnd41	blood
2	chr20:13651000-13653000	Enhancers	Thymus	Thymus
3	chr20:13651000-13653200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:13651400-13653600	Enhancers	Fetal Lung	lung
5	chr20:13651600-13654200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr20:13651800-13653600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:13651800-13654000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:13651800-13654000	Enhancers	Osteobl	bone
9	chr20:13652200-13653600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr20:13652400-13653200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:13652400-13653200	Weak transcription	Aorta	Aorta
12	chr20:13652400-13653400	Enhancers	HSMM	muscle
13	chr20:13652600-13653000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:13652800-13653600	Enhancers	Adipose Nuclei	Adipose
15	chr20:13652800-13653800	Enhancers	Liver	Liver
16	chr20:13652800-13656800	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links