Variant report

Variant	rs12099691
Chromosome Location	chr12:25484555-25484556
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:14)

rs_ID	r²[population]
rs10505973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11047969	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11047974	1.00[AMR][1000 genomes]
rs11047975	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12298887	1.00[MEX][hapmap]
rs12308451	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12309390	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16928744	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1904389	1.00[GIH][hapmap]
rs56145890	1.00[AMR][1000 genomes]
rs56231104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59763974	0.85[AMR][1000 genomes]
rs61453941	1.00[AMR][1000 genomes]
rs7135826	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898928	chr12:25458354-25499342	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv976719	chr12:25482467-25552186	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12099691	PPP4R4	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25475800-25486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:25476000-25485600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:25476800-25486800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:25477000-25485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:25477000-25486600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:25477400-25486800	Weak transcription	NH-A	brain
7	chr12:25477400-25487400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:25478000-25484600	Weak transcription	GM12878-XiMat	blood
9	chr12:25481400-25486800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:25481800-25485800	Weak transcription	Hela-S3	cervix
11	chr12:25482000-25486800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:25482200-25485800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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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