Variant report

Variant	rs6048911
Chromosome Location	chr20:23568008-23568009
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23562870..23565685-chr20:23566645..23569407,3	K562	blood:
2	chr20:23329684..23331925-chr20:23566520..23568100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132661	Chromatin interaction
ENSG00000204658	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1467502	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1973958	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56081987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56094881	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57311633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58762270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6036456	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6036457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6036458	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048895	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048898	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048903	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048909	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048910	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6048913	0.82[AFR][1000 genomes]
rs61701236	0.87[AMR][1000 genomes]
rs73904938	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23562200-23568200	Enhancers	HMEC	breast
2	chr20:23562400-23568200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:23562600-23568200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:23565000-23568600	Enhancers	Esophagus	oesophagus
5	chr20:23565400-23568400	Enhancers	Fetal Intestine Large	intestine
6	chr20:23565400-23568400	Enhancers	Fetal Intestine Small	intestine
7	chr20:23566000-23568400	Flanking Active TSS	HepG2	liver
8	chr20:23566800-23568200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:23566800-23568600	Enhancers	Placenta	Placenta
10	chr20:23567200-23569200	Weak transcription	Fetal Thymus	thymus
11	chr20:23567600-23569000	Weak transcription	Stomach Mucosa	stomach
12	chr20:23568000-23569200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:23568000-23569400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links