Variant report

Variant	rs59512557
Chromosome Location	chr20:25377342-25377343
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	chr20:25367909..25369647-chr20:25375596..25377784,2	MCF-7	breast:
2	chr20:25377062..25378773-chr20:25386652..25389539,2	K562	blood:

Variant related genes	Relation type
ENSG00000101003	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11087514	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28565216	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28714346	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35054550	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56964222	0.83[AMR][1000 genomes]
rs57167788	0.83[AMR][1000 genomes]
rs57273246	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57284766	0.83[AMR][1000 genomes]
rs57286322	0.83[AMR][1000 genomes]
rs57365695	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57734297	0.83[AMR][1000 genomes]
rs57822703	0.83[AMR][1000 genomes]
rs57918703	0.83[AMR][1000 genomes]
rs57956383	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57974728	0.83[AMR][1000 genomes]
rs58167480	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58476027	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58577156	0.83[AMR][1000 genomes]
rs58828776	0.83[AMR][1000 genomes]
rs59001189	0.83[AMR][1000 genomes]
rs59002519	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59107453	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59124158	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59172682	0.83[AMR][1000 genomes]
rs59319689	0.83[AMR][1000 genomes]
rs59366271	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59444992	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59802545	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59813927	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59846731	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59887855	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59894298	0.83[AMR][1000 genomes]
rs60054780	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60505561	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61170040	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61416782	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61446016	0.83[AMR][1000 genomes]
rs7261761	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7264886	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7265940	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7266057	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7272247	0.83[AMR][1000 genomes]
rs7272899	0.83[AMR][1000 genomes]
rs8124309	0.83[AFR][1000 genomes]
rs8126155	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9784192	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv964440	chr20:25351740-25387631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25372000-25378000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr20:25372000-25379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25372200-25377600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr20:25372200-25377600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:25372200-25379000	Weak transcription	Brain Angular Gyrus	brain
6	chr20:25372200-25379000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:25372200-25380800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:25372400-25377800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:25372400-25379000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr20:25372400-25379200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr20:25374800-25379400	Weak transcription	Hela-S3	cervix
12	chr20:25375000-25379200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr20:25375000-25379200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr20:25375200-25379200	Weak transcription	Brain Hippocampus Middle	brain
15	chr20:25375200-25379200	Weak transcription	Brain Substantia Nigra	brain
16	chr20:25375400-25379000	Weak transcription	Brain Anterior Caudate	brain
17	chr20:25375400-25379600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr20:25375800-25379200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:25376000-25377600	Weak transcription	GM12878-XiMat	blood
20	chr20:25376000-25379000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:25377000-25378000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:25377200-25377400	Weak transcription	Colonic Mucosa	Colon

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