Variant report

Variant	rs563516
Chromosome Location	chr15:53941900-53941901
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs16966321	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16966332	0.93[AFR][1000 genomes]
rs16966340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16966343	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16966345	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16966348	0.87[AFR][1000 genomes]
rs16966350	0.90[AFR][1000 genomes]
rs1906408	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2447055	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2450826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2614210	0.89[AFR][1000 genomes]
rs2633249	0.90[AFR][1000 genomes]
rs2633250	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2926880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2926882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2926883	0.85[AFR][1000 genomes]
rs2926884	0.90[AFR][1000 genomes]
rs3985793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4776166	0.80[AFR][1000 genomes]
rs526055	0.90[AFR][1000 genomes]
rs546516	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56195724	0.85[AFR][1000 genomes]
rs56372661	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57223417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59055966	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60459339	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60652242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61302170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61611399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689638	0.92[AFR][1000 genomes]
rs689785	0.92[AFR][1000 genomes]
rs689811	0.92[AFR][1000 genomes]
rs689845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs690112	0.92[AFR][1000 genomes]
rs690120	0.89[AFR][1000 genomes]
rs690205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs690447	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs690509	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs690610	0.90[AFR][1000 genomes]
rs73408266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408269	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408271	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408292	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73408295	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408297	0.88[AFR][1000 genomes]
rs74015841	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv569435	chr15:53845097-53966805	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv934282	chr15:53872148-53989432	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv527474	chr15:53874591-53991833	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1043995	chr15:53907679-53968209	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv833010	chr15:53935652-54099849	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	nsv569443	chr15:53936907-53972798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53927200-53951400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:53941200-53943400	Enhancers	Liver	Liver

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