Variant report

Variant	rs6023394
Chromosome Location	chr20:53214393-53214394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53213011..53216451-chr20:53226919..53231866,4	MCF-7	breast:
2	chr14:58059742..58061495-chr20:53212629..53215482,2	MCF-7	breast:
3	chr20:53201780..53208417-chr20:53214130..53221252,9	MCF-7	breast:
4	chr20:53212235..53214579-chr20:53217429..53220082,3	MCF-7	breast:
5	chr20:53212410..53215334-chr20:53259205..53262055,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16999893	0.83[AMR][1000 genomes]
rs2169707	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28663252	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55705559	0.83[EUR][1000 genomes]
rs56138015	0.83[EUR][1000 genomes]
rs56294816	0.83[EUR][1000 genomes]
rs58298733	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60030360	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014066	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014067	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6014073	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014074	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6014075	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6014076	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6014077	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6014078	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014080	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014098	0.83[AMR][1000 genomes]
rs6023382	0.83[AMR][1000 genomes]
rs6023383	0.80[AMR][1000 genomes]
rs6023384	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023385	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6023386	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023387	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6023388	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6023396	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023397	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023398	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023401	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023403	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6068912	0.93[YRI][hapmap]
rs6091925	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs6098103	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098104	0.83[EUR][1000 genomes]
rs6098105	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098111	0.84[EUR][1000 genomes]
rs7269966	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7270971	0.83[YRI][hapmap]
rs73144063	0.84[EUR][1000 genomes]
rs73144072	0.83[EUR][1000 genomes]
rs73144079	0.83[EUR][1000 genomes]
rs73144086	0.83[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
3	chr20:53206400-53226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:53206600-53214800	Weak transcription	Aorta	Aorta
5	chr20:53206600-53216600	Weak transcription	Fetal Brain Female	brain
6	chr20:53207200-53217000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr20:53208800-53214400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr20:53209000-53215600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr20:53209000-53216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:53209800-53216200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:53210800-53216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:53213200-53217000	Weak transcription	Psoas Muscle	Psoas
13	chr20:53213800-53214800	Weak transcription	Brain Germinal Matrix	brain
14	chr20:53214200-53215000	Enhancers	Fetal Brain Male	brain

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