Variant report

Variant	rs28558229
Chromosome Location	chr14:25264404-25264405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10144442	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10144620	0.94[EUR][1000 genomes]
rs12587304	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12589949	0.93[EUR][1000 genomes]
rs28393479	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28510104	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28623432	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9323559	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652368	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1046542	chr14:25244806-25267208	Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1045403	chr14:25249822-25271815	Enhancers Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3527118	chr14:25260312-25264710	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv564068	chr14:25262373-25264662	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv564070	chr14:25262527-25264662	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28558229	LRRC16	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25261800-25268200	Weak transcription	Fetal Lung	lung
2	chr14:25263800-25264600	Enhancers	Fetal Brain Male	brain
3	chr14:25264400-25264600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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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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