Variant report

Variant	rs3092648
Chromosome Location	chr20:41685538-41685539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49658404..49658949-chr20:41685431..41685931,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1106978	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1157154	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2208048	0.82[EUR][1000 genomes]
rs2208049	0.81[EUR][1000 genomes]
rs2425545	0.82[EUR][1000 genomes]
rs2425546	0.82[EUR][1000 genomes]
rs2425547	0.82[EUR][1000 genomes]
rs2425549	0.82[EUR][1000 genomes]
rs2425550	0.82[EUR][1000 genomes]
rs2425551	0.82[EUR][1000 genomes]
rs2425552	0.81[EUR][1000 genomes]
rs2425553	0.82[EUR][1000 genomes]
rs2425554	0.82[EUR][1000 genomes]
rs2425555	0.82[EUR][1000 genomes]
rs2425556	0.82[EUR][1000 genomes]
rs2425557	0.82[EUR][1000 genomes]
rs2425558	0.80[EUR][1000 genomes]
rs2425559	0.83[EUR][1000 genomes]
rs2425560	0.83[EUR][1000 genomes]
rs2425561	0.83[EUR][1000 genomes]
rs2425563	0.83[EUR][1000 genomes]
rs2425564	0.83[EUR][1000 genomes]
rs2425565	0.83[EUR][1000 genomes]
rs2425566	0.81[EUR][1000 genomes]
rs2425567	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2425568	0.82[EUR][1000 genomes]
rs2425570	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2425572	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2425573	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2425574	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3091443	0.80[EUR][1000 genomes]
rs3091548	0.82[EUR][1000 genomes]
rs3091580	0.80[EUR][1000 genomes]
rs3091581	0.82[EUR][1000 genomes]
rs3091752	0.83[EUR][1000 genomes]
rs3091800	0.80[EUR][1000 genomes]
rs3091990	0.83[EUR][1000 genomes]
rs3092089	0.95[ASN][1000 genomes]
rs3092095	0.83[EUR][1000 genomes]
rs3092117	0.83[EUR][1000 genomes]
rs3092156	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092177	0.80[EUR][1000 genomes]
rs3092215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092328	0.82[EUR][1000 genomes]
rs3092568	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3092739	0.83[EUR][1000 genomes]
rs4444608	0.82[EUR][1000 genomes]
rs713108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910829	0.83[EUR][1000 genomes]
rs910830	0.83[EUR][1000 genomes]
rs927054	0.82[EUR][1000 genomes]
rs927056	0.82[EUR][1000 genomes]
rs984962	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996478	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998739	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060468	chr20:41518010-41700012	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1061053	chr20:41521471-41704874	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv949221	chr20:41594025-41742176	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv869774	chr20:41595567-41746533	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2762078	chr20:41598181-41745491	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv948829	chr20:41598995-41742176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1065908	chr20:41620966-41735969	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41674000-41700600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:41684800-41685600	Enhancers	Colon Smooth Muscle	Colon
3	chr20:41685200-41687600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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