Variant report

Variant	rs6023422
Chromosome Location	chr20:53240284-53240285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:53239460..53242242-chr20:53249088..53250613,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10154005	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10485784	0.86[AMR][1000 genomes]
rs13433172	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16999893	0.82[EUR][1000 genomes]
rs55705559	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55960128	0.93[AMR][1000 genomes]
rs56138015	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56187828	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56294816	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56371656	0.93[AMR][1000 genomes]
rs57120787	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6014087	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6014089	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6014098	0.82[EUR][1000 genomes]
rs6023396	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6091933	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6091939	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6098093	0.83[AMR][1000 genomes]
rs6098099	0.87[AMR][1000 genomes]
rs6098104	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6098111	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6098116	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6098118	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6098123	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6098129	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6098130	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62214433	0.90[AMR][1000 genomes]
rs68183459	0.80[EUR][1000 genomes]
rs73140147	0.86[AMR][1000 genomes]
rs73144055	0.97[AMR][1000 genomes]
rs73144063	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73144072	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73144079	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73144086	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73146053	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73146055	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73146076	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
2	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:53229200-53240600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:53235000-53241600	Enhancers	Fetal Brain Male	brain
5	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
6	chr20:53236000-53241800	Weak transcription	Pancreas	Pancrea
7	chr20:53236200-53240600	Weak transcription	Right Atrium	heart
8	chr20:53236200-53240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:53236400-53240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:53238200-53241000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr20:53238400-53241000	Enhancers	Fetal Brain Female	brain
13	chr20:53238400-53242000	Enhancers	Fetal Muscle Trunk	muscle
14	chr20:53238400-53242800	Enhancers	Fetal Muscle Leg	muscle
15	chr20:53238600-53242400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:53238800-53242400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr20:53238800-53242800	Enhancers	Fetal Lung	lung
18	chr20:53239000-53240600	Enhancers	Brain Substantia Nigra	brain
19	chr20:53239000-53241000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr20:53239000-53241200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr20:53239200-53242000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:53239200-53242000	Enhancers	Brain Angular Gyrus	brain
23	chr20:53239400-53240400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:53239400-53240400	Weak transcription	Brain Hippocampus Middle	brain
25	chr20:53239400-53240400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr20:53239400-53240400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr20:53239400-53240600	Weak transcription	Fetal Heart	heart
28	chr20:53239400-53240600	Weak transcription	Fetal Stomach	stomach
29	chr20:53239400-53241400	Enhancers	NHDF-Ad	bronchial
30	chr20:53239600-53240600	Weak transcription	Brain Anterior Caudate	brain
31	chr20:53239600-53240800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:53240000-53240400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:53240000-53240800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr20:53240000-53241000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr20:53240000-53241200	Weak transcription	NH-A	brain
36	chr20:53240200-53240600	Enhancers	Brain Germinal Matrix	brain
37	chr20:53240200-53240800	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links