Variant report

Variant	rs12999804
Chromosome Location	chr2:31245650-31245651
allele	A/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:17)

rs_ID	r²[population]
rs10198054	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10207139	0.92[YRI][hapmap]
rs10209881	0.87[ASW][hapmap];0.81[YRI][hapmap]
rs12473730	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs12613732	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621546	0.87[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs13009779	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1862966	0.80[ASW][hapmap]
rs1862967	0.80[ASW][hapmap]
rs2194455	0.87[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4245765	0.91[EUR][1000 genomes]
rs4245766	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4951960	0.82[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5009910	0.80[ASW][hapmap];0.83[MEX][hapmap]
rs6543594	0.88[MEX][hapmap]
rs7605982	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs9308914	0.82[ASW][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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12999804	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31232600-31251000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:31235200-31251000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:31235400-31251000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:31236400-31249400	Weak transcription	NHEK	skin
5	chr2:31245600-31246200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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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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