Variant report

Variant	rs6097782
Chromosome Location	chr20:52751545-52751546
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:49346111..49348887-chr20:52750749..52752631,2	MCF-7	breast:
2	chr20:46413224..46418685-chr20:52746491..52752686,10	MCF-7	breast:
3	chr20:52749844..52752672-chrX:76227808..76229967,2	MCF-7	breast:
4	chr20:52749860..52752197-chr8:108092484..108095332,2	MCF-7	breast:
5	chr17:56735202..56737939-chr20:52748696..52751920,4	MCF-7	breast:
6	chr20:52749967..52752847-chr20:52755293..52758111,2	K562	blood:
7	chr20:52720225..52723216-chr20:52749431..52752183,2	K562	blood:
8	chr17:56707619..56710651-chr20:52747363..52752620,6	MCF-7	breast:
9	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
10	chr20:52749818..52752750-chr5:43554749..43557451,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000196562	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11905401	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11906715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11907046	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11907150	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11907800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11907836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16999008	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886308	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1977297	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2274131	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4809955	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4811492	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4811493	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55733210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56353101	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57016987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57562389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57623780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57865579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58978141	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59078348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59684245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60250398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6091819	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6091820	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097783	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097790	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097793	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097794	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097796	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097797	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097801	0.92[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62214481	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66870448	0.94[ASN][1000 genomes]
rs7263855	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751090	0.89[ASN][1000 genomes]
rs8114002	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8114105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8117971	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8118066	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8118441	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873216	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6097782	C20orf107	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr20:52748800-52751600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:52749400-52751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:52749400-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:52750200-52751600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:52750200-52751800	Enhancers	Hela-S3	cervix
8	chr20:52750200-52756600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr20:52750400-52751600	Enhancers	Osteobl	bone
10	chr20:52750600-52751800	Enhancers	HepG2	liver
11	chr20:52750800-52751800	Enhancers	NH-A	brain
12	chr20:52750800-52755800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52751000-52756600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr20:52751200-52758000	Weak transcription	Placenta	Placenta
15	chr20:52751400-52751600	Weak transcription	NHLF	lung
16	chr20:52751400-52751800	Enhancers	NHEK	skin
17	chr20:52751400-52754400	ZNF genes & repeats	A549	lung
18	chr20:52751400-52755800	Weak transcription	NHDF-Ad	bronchial
19	chr20:52751400-52756200	Weak transcription	HSMM	muscle
20	chr20:52751400-52757000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr20:52751400-52757200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr20:52751400-52758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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