Variant report

Variant	rs16904090
Chromosome Location	chr8:130499223-130499224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10097701	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11779103	0.85[EUR][1000 genomes]
rs12677044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12681345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16893242	0.88[ASW][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs16904082	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16904087	0.87[EUR][1000 genomes]
rs16904093	0.86[EUR][1000 genomes]
rs16904094	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1897682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1897683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs57568551	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60235966	0.84[EUR][1000 genomes]
rs61677427	0.86[EUR][1000 genomes]
rs973006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015611	chr8:130449321-130502086	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16904090	PHF20L1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130490200-130503400	Weak transcription	Dnd41	blood
2	chr8:130495600-130499600	Genic enhancers	K562	blood
3	chr8:130497200-130504200	Weak transcription	Thymus	Thymus
4	chr8:130497600-130500800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr8:130497600-130501000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr8:130497600-130503600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:130499000-130499800	Enhancers	Fetal Muscle Leg	muscle

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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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