Variant report

Variant	rs12185625
Chromosome Location	chr2:234875433-234875434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234861030..234863586-chr2:234874860..234877579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144481	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10490016	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12995095	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13024825	1.00[JPT][hapmap]
rs17863853	0.94[EUR][1000 genomes]
rs6709823	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6760498	0.88[CEU][hapmap];0.86[EUR][1000 genomes]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12185625	AGAP1	cis	cerebellum	SCAN
rs12185625	NMUR1	cis	parietal	SCAN
rs12185625	FBXO36	cis	cerebellum	SCAN
rs12185625	IQCA1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234849400-234883400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:234862600-234882200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:234863000-234882200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:234873600-234875800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:234874000-234876000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:234874000-234879400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:234874800-234876200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:234875000-234875600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:234875000-234875800	Enhancers	Brain Anterior Caudate	brain
10	chr2:234875000-234875800	Enhancers	HSMM	muscle
11	chr2:234875000-234876200	Enhancers	Brain Angular Gyrus	brain
12	chr2:234875000-234876200	Enhancers	Brain Hippocampus Middle	brain
13	chr2:234875000-234876400	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:234875000-234878000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:234875200-234877600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:234875200-234877600	Enhancers	Thymus	Thymus
17	chr2:234875400-234875800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:234875400-234875800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:234875400-234876200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:234875400-234876200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:234875400-234876400	Enhancers	HSMMtube	muscle

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