Variant report

Variant	rs59925877
Chromosome Location	chr13:87840408-87840409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLITRK5-17	chr13:87840003-87840983	NONHSAT034582

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs3963903	1.00[AMR][1000 genomes]
rs4511400	1.00[AMR][1000 genomes]
rs4553471	1.00[AMR][1000 genomes]
rs4575405	1.00[AMR][1000 genomes]
rs55758789	0.85[AMR][1000 genomes]
rs55811630	0.85[AMR][1000 genomes]
rs56036938	0.85[AMR][1000 genomes]
rs56702454	0.85[AMR][1000 genomes]
rs56814755	0.85[AMR][1000 genomes]
rs56858752	0.85[AMR][1000 genomes]
rs56970807	0.85[AMR][1000 genomes]
rs57019306	0.85[AMR][1000 genomes]
rs57289088	0.85[AMR][1000 genomes]
rs57704092	1.00[AMR][1000 genomes]
rs57871348	0.85[AMR][1000 genomes]
rs58436419	0.85[AMR][1000 genomes]
rs58514415	0.85[AMR][1000 genomes]
rs58833676	0.85[AMR][1000 genomes]
rs59046442	1.00[AMR][1000 genomes]
rs59092487	1.00[AMR][1000 genomes]
rs59102208	0.85[AMR][1000 genomes]
rs59699555	0.85[AMR][1000 genomes]
rs60065293	0.85[AMR][1000 genomes]
rs60314271	1.00[AMR][1000 genomes]
rs60475582	0.85[AMR][1000 genomes]
rs60516314	0.85[AMR][1000 genomes]
rs60632788	0.85[AMR][1000 genomes]
rs60967936	0.85[AMR][1000 genomes]
rs61001114	0.85[AMR][1000 genomes]
rs61607055	0.85[AMR][1000 genomes]
rs61613775	0.85[AMR][1000 genomes]
rs61711434	0.85[AMR][1000 genomes]
rs73558873	0.85[AMR][1000 genomes]
rs73558881	0.85[AMR][1000 genomes]
rs73558888	0.85[AMR][1000 genomes]
rs73558889	0.85[AMR][1000 genomes]
rs73558892	0.85[AMR][1000 genomes]
rs73558894	0.85[AMR][1000 genomes]
rs73558897	0.85[AMR][1000 genomes]
rs73560614	0.85[AMR][1000 genomes]
rs73560615	0.85[AMR][1000 genomes]
rs73560618	0.85[AMR][1000 genomes]
rs73560626	0.85[AMR][1000 genomes]
rs73560628	0.85[AMR][1000 genomes]
rs73560690	0.85[AMR][1000 genomes]
rs73560692	0.85[AMR][1000 genomes]
rs73560695	0.85[AMR][1000 genomes]
rs73560696	1.00[AMR][1000 genomes]
rs73560700	1.00[AMR][1000 genomes]
rs73561058	0.85[AMR][1000 genomes]
rs73561062	0.85[AMR][1000 genomes]
rs73561063	0.85[AMR][1000 genomes]
rs73561064	0.85[AMR][1000 genomes]
rs73561067	0.85[AMR][1000 genomes]
rs73561074	0.85[AMR][1000 genomes]
rs73561076	0.85[AMR][1000 genomes]
rs73561079	0.85[AMR][1000 genomes]
rs73561089	0.85[AMR][1000 genomes]
rs73561097	0.85[AMR][1000 genomes]
rs73562405	1.00[AMR][1000 genomes]
rs73562409	1.00[AMR][1000 genomes]
rs73562411	1.00[AMR][1000 genomes]
rs73562418	1.00[AMR][1000 genomes]
rs73562421	1.00[AMR][1000 genomes]
rs73562428	1.00[AMR][1000 genomes]
rs73563113	0.85[AMR][1000 genomes]
rs73565477	0.85[AMR][1000 genomes]
rs73565483	0.85[AMR][1000 genomes]
rs73565494	1.00[AMR][1000 genomes]
rs73565498	1.00[AMR][1000 genomes]
rs73566070	0.85[AMR][1000 genomes]
rs73566071	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73566074	0.85[AMR][1000 genomes]
rs73566083	0.85[AMR][1000 genomes]
rs73566089	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73566091	0.85[AMR][1000 genomes]
rs73566098	0.85[AMR][1000 genomes]
rs73566100	0.85[AMR][1000 genomes]
rs73567606	0.85[AMR][1000 genomes]
rs74103265	0.85[AMR][1000 genomes]
rs74103273	0.85[AMR][1000 genomes]
rs74103280	0.85[AMR][1000 genomes]
rs74103287	0.85[AMR][1000 genomes]
rs74103289	0.85[AMR][1000 genomes]
rs74103291	0.85[AMR][1000 genomes]
rs74103357	0.85[AMR][1000 genomes]
rs74103367	0.85[AMR][1000 genomes]
rs74103376	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv562621	chr13:87192747-87927450	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1045687	chr13:87822969-88114685	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv541860	chr13:87822969-88114685	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3351770	chr13:87824000-87847009	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
5	nsv930999	chr13:87831662-88143592	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1047914	chr13:87835419-87909531	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1043448	chr13:87835419-88140970	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv517795	chr13:87836852-87893390	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:87838800-87840600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:87839800-87840800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr13:87839800-87842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:87839800-87842600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:87840200-87841200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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