Variant report

Variant	rs60250398
Chromosome Location	chr20:52750730-52750731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:57913131..57926939-chr20:52735776..52751538,42	MCF-7	breast:
2	chr20:46640095..46644047-chr20:52746837..52750756,3	MCF-7	breast:
3	chr20:46413224..46418685-chr20:52746491..52752686,10	MCF-7	breast:
4	chr12:53344317..53347285-chr20:52748753..52751041,2	MCF-7	breast:
5	chr20:52749844..52752672-chrX:76227808..76229967,2	MCF-7	breast:
6	chr20:52748698..52751291-chr5:43063719..43066495,2	MCF-7	breast:
7	chr1:184044285..184045279-chr20:52750627..52751499,2	MCF-7	breast:
8	chr20:52749860..52752197-chr8:108092484..108095332,2	MCF-7	breast:
9	chr17:56735202..56737939-chr20:52748696..52751920,4	MCF-7	breast:
10	chr20:52749967..52752847-chr20:52755293..52758111,2	K562	blood:
11	chr17:56736366..56738088-chr20:52748194..52751006,3	MCF-7	breast:
12	chr17:46114293..46114952-chr20:52750236..52751200,2	MCF-7	breast:
13	chr20:52720225..52723216-chr20:52749431..52752183,2	K562	blood:
14	chr20:46616780..46618691-chr20:52748141..52750829,2	MCF-7	breast:
15	chr17:56707619..56710651-chr20:52747363..52752620,6	MCF-7	breast:
16	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
17	chr20:52749818..52752750-chr5:43554749..43557451,2	MCF-7	breast:
18	chr15:63794674..63797406-chr20:52748938..52750854,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000225410	Chromatin interaction
ENSG00000207947	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000140455	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000237423	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000265039	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11905401	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11907046	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11907150	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11907800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11907836	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16999008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1977297	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2274131	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4809955	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4811492	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4811493	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55733210	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56353101	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57016987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57562389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57623780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57865579	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58978141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59078348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59684245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6097782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097783	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097791	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097792	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097794	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097796	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097797	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097801	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62214481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66870448	0.98[ASN][1000 genomes]
rs7263855	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751090	0.94[ASN][1000 genomes]
rs8114002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114105	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8118066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8118441	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs873216	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2296359	chr20:52750391-52750832	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52748200-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr20:52748200-52751800	Enhancers	HMEC	breast
3	chr20:52748400-52750800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr20:52748400-52751400	Enhancers	NHLF	lung
5	chr20:52748800-52751000	Flanking Active TSS	A549	lung
6	chr20:52748800-52751600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:52749400-52751400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr20:52749400-52751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:52749400-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:52750200-52751000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr20:52750200-52751000	Weak transcription	Placenta	Placenta
12	chr20:52750200-52751400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:52750200-52751400	Enhancers	HSMM	muscle
14	chr20:52750200-52751600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:52750200-52751800	Enhancers	Hela-S3	cervix
16	chr20:52750200-52756600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:52750400-52750800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:52750400-52750800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr20:52750400-52751400	Enhancers	NHDF-Ad	bronchial
20	chr20:52750400-52751600	Enhancers	Osteobl	bone
21	chr20:52750600-52750800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:52750600-52750800	Flanking Active TSS	NH-A	brain
23	chr20:52750600-52750800	Flanking Active TSS	NHEK	skin
24	chr20:52750600-52751800	Enhancers	HepG2	liver

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