Variant report

Variant	rs12858615
Chromosome Location	chr13:54980688-54980689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12429754	0.82[EUR][1000 genomes]
rs1336988	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591606	0.99[EUR][1000 genomes]
rs4439639	0.81[AFR][1000 genomes]
rs4517664	0.80[AFR][1000 genomes]
rs61954786	0.98[EUR][1000 genomes]
rs7322723	0.86[AFR][1000 genomes]
rs7328189	0.93[EUR][1000 genomes]
rs7331944	0.86[EUR][1000 genomes]
rs7335107	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336253	0.93[EUR][1000 genomes]
rs7489856	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985620	0.84[AFR][1000 genomes]
rs9536717	0.83[AFR][1000 genomes]
rs9569023	0.95[EUR][1000 genomes]
rs9569029	0.96[EUR][1000 genomes]
rs9569033	0.96[EUR][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	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr13:54969000-54980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:54969600-54982400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:54976800-54982600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr13:54977600-54983000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:54979000-54980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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