Variant report

Variant	rs6050480
Chromosome Location	chr20:25224370-25224371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr20:25224190-25224549	U2OS	brain:	n/a	n/a
2	POLR2A	chr20:25224331-25225922	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25201569..25205371-chr20:25224362..25226841,4	MCF-7	breast:
2	chr20:25223963..25226805-chr20:25228679..25230694,3	K562	blood:

Variant related genes	Relation type
PYGB	TF binding region
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs2258671	0.83[AFR][1000 genomes]
rs2258672	0.83[AFR][1000 genomes]
rs2474768	0.89[AFR][1000 genomes]
rs2474770	0.89[AFR][1000 genomes]
rs2474772	0.89[AFR][1000 genomes]
rs2474775	0.83[AFR][1000 genomes]
rs2482920	0.81[AFR][1000 genomes]
rs2500411	0.85[AFR][1000 genomes]
rs2500429	0.83[AFR][1000 genomes]
rs2500431	0.81[AFR][1000 genomes]
rs2983490	0.87[AFR][1000 genomes]
rs3002699	0.81[AFR][1000 genomes]
rs3002700	0.81[AFR][1000 genomes]
rs55879612	1.00[AMR][1000 genomes]
rs56063344	1.00[AMR][1000 genomes]
rs56343188	1.00[AMR][1000 genomes]
rs56374952	1.00[AMR][1000 genomes]
rs57359365	1.00[AMR][1000 genomes]
rs57509861	1.00[AMR][1000 genomes]
rs58134777	1.00[AMR][1000 genomes]
rs6037066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050467	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61245897	1.00[AMR][1000 genomes]
rs73904004	1.00[AMR][1000 genomes]
rs73904009	1.00[AMR][1000 genomes]
rs73904014	1.00[AMR][1000 genomes]
rs73904015	1.00[AMR][1000 genomes]
rs73904016	1.00[AMR][1000 genomes]
rs73904018	1.00[AMR][1000 genomes]
rs73904030	1.00[AMR][1000 genomes]
rs73904034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904035	1.00[AMR][1000 genomes]
rs73904036	0.87[AFR][1000 genomes]
rs73904038	0.89[AFR][1000 genomes]
rs73904039	0.89[AFR][1000 genomes]
rs73904040	1.00[AMR][1000 genomes]
rs73904467	1.00[AMR][1000 genomes]
rs73904468	1.00[AMR][1000 genomes]
rs73904472	1.00[AMR][1000 genomes]
rs73906090	1.00[AMR][1000 genomes]
rs73907308	1.00[AMR][1000 genomes]
rs73907312	1.00[AMR][1000 genomes]
rs73907315	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv828708	chr20:25223895-25231601	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25217600-25227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:25219000-25226000	Weak transcription	Colonic Mucosa	Colon
3	chr20:25219000-25227400	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:25219400-25226800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:25219400-25226800	Weak transcription	Right Ventricle	heart
6	chr20:25219400-25227600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:25219400-25228000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr20:25219600-25227000	Weak transcription	NHDF-Ad	bronchial
9	chr20:25219800-25227400	Weak transcription	NHLF	lung
10	chr20:25220200-25227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr20:25220400-25227400	Weak transcription	Esophagus	oesophagus
12	chr20:25220600-25226800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:25220600-25227200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr20:25220800-25226000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:25221800-25225800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr20:25221800-25226000	Weak transcription	Fetal Heart	heart
17	chr20:25221800-25226800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr20:25221800-25226800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:25222000-25226200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr20:25222000-25226800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:25222000-25227000	Weak transcription	HSMM	muscle
22	chr20:25222000-25227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:25222000-25227400	Weak transcription	Fetal Kidney	kidney
24	chr20:25222000-25227400	Weak transcription	HSMMtube	muscle
25	chr20:25222000-25227600	Weak transcription	Fetal Lung	lung
26	chr20:25222400-25227000	Weak transcription	K562	blood
27	chr20:25222400-25227400	Weak transcription	NH-A	brain
28	chr20:25222600-25224400	Enhancers	HMEC	breast
29	chr20:25223000-25225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:25223200-25224400	Weak transcription	A549	lung
31	chr20:25223200-25227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr20:25223400-25226000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:25223400-25227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:25223600-25225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr20:25223600-25227800	Weak transcription	Brain Germinal Matrix	brain
36	chr20:25223800-25227600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr20:25224200-25224600	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr20:25224200-25225200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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