Variant report

Variant	rs16986489
Chromosome Location	chr22:28900677-28900678
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:8)

rs_ID	r²[population]
rs16986354	0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs16986420	0.82[JPT][hapmap];0.84[MEX][hapmap];0.91[AMR][1000 genomes]
rs16986431	0.84[MEX][hapmap];0.97[AMR][1000 genomes]
rs16986442	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16986544	0.84[AMR][1000 genomes]
rs16987010	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs4615019	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4638900	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16986489	NCRNA00200	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28893000-28901600	Weak transcription	Psoas Muscle	Psoas
2	chr22:28893600-28901400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr22:28894600-28901400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:28899400-28901400	Weak transcription	Dnd41	blood
5	chr22:28899600-28904000	Weak transcription	Fetal Lung	lung
6	chr22:28900600-28900800	Enhancers	HSMMtube	muscle

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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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