Variant report

Variant	rs6563138
Chromosome Location	chr13:80411823-80411824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12584575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6563144	1.00[CEU][hapmap];0.88[MEX][hapmap]
rs6563145	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7139668	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7321144	0.84[AMR][1000 genomes]
rs73224591	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7324097	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9545243	1.00[CEU][hapmap]
rs996382	0.83[AMR][1000 genomes];0.84[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	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900590	chr13:80342186-80421340	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1043768	chr13:80398379-80447095	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6563138	FAM54B	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80410200-80412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr13:80411200-80412400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:80411200-80413000	Enhancers	Hela-S3	cervix
4	chr13:80411400-80412600	Enhancers	NH-A	brain
5	chr13:80411600-80412000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:80411600-80412000	Enhancers	HMEC	breast
7	chr13:80411600-80412200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:80411600-80412600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:80411600-80412600	Enhancers	HSMM	muscle
10	chr13:80411600-80412600	Enhancers	HSMMtube	muscle
11	chr13:80411600-80412600	Enhancers	NHDF-Ad	bronchial
12	chr13:80411600-80413000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr13:80411800-80412000	Enhancers	NHLF	lung
14	chr13:80411800-80412200	Enhancers	Osteobl	bone

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Input of quick search could be:

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

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