Variant report

Variant	rs16858133
Chromosome Location	chr2:12138656-12138657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12478633	0.84[EUR][1000 genomes]
rs12478664	0.84[EUR][1000 genomes]
rs12478705	0.84[EUR][1000 genomes]
rs13012119	0.84[EUR][1000 genomes]
rs13025618	0.99[EUR][1000 genomes]
rs34163220	0.89[AFR][1000 genomes]
rs34424904	0.99[EUR][1000 genomes]
rs34774368	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35951700	0.94[EUR][1000 genomes]
rs41378155	0.84[EUR][1000 genomes]
rs62113775	0.84[EUR][1000 genomes]
rs62113776	0.84[EUR][1000 genomes]
rs62116478	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62116484	0.90[EUR][1000 genomes]
rs71446446	0.98[EUR][1000 genomes]

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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16858133	ID2	cis	cerebellum	SCAN
rs16858133	SPP1	trans	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12134800-12139800	Enhancers	NHDF-Ad	bronchial
2	chr2:12135200-12139600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:12135200-12139800	Enhancers	HSMM	muscle
4	chr2:12135400-12139400	Enhancers	Osteobl	bone
5	chr2:12135600-12138800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:12136400-12139400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:12136800-12138800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:12136800-12139400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:12137200-12148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:12137400-12140200	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:12137800-12138800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:12137800-12138800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:12137800-12139000	Enhancers	Dnd41	blood
14	chr2:12137800-12139000	Enhancers	HUVEC	blood vessel
15	chr2:12138000-12138800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:12138000-12138800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:12138000-12139200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:12138000-12139600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:12138000-12139600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:12138000-12139600	Flanking Active TSS	GM12878-XiMat	blood
21	chr2:12138000-12140200	Enhancers	HSMMtube	muscle
22	chr2:12138200-12139000	Enhancers	Primary T cells from cord blood	blood
23	chr2:12138200-12139200	Enhancers	NHLF	lung
24	chr2:12138400-12138800	Enhancers	NH-A	brain
25	chr2:12138400-12139600	Enhancers	Fetal Muscle Leg	muscle
26	chr2:12138400-12139800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:12138400-12139800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:12138600-12139000	Enhancers	HMEC	breast
29	chr2:12138600-12139200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:12138600-12142000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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