Variant report

Variant	rs12139468
Chromosome Location	chr1:222183756-222183757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221914275..221916996-chr1:222181914..222184462,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11118920	0.93[EUR][1000 genomes]
rs11118930	0.88[EUR][1000 genomes]
rs11118931	0.90[EUR][1000 genomes]
rs12031848	0.85[EUR][1000 genomes]
rs12117316	0.92[ASN][1000 genomes]
rs1339870	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1416896	0.94[EUR][1000 genomes]
rs1470233	0.90[EUR][1000 genomes]
rs2053510	0.90[EUR][1000 genomes]
rs2053511	0.92[EUR][1000 genomes]
rs2053512	0.88[EUR][1000 genomes]
rs2378499	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2584314	0.89[EUR][1000 genomes]
rs2584315	0.89[EUR][1000 genomes]
rs2584316	0.89[EUR][1000 genomes]
rs2584317	0.91[EUR][1000 genomes]
rs2584318	0.90[EUR][1000 genomes]
rs2584319	0.90[EUR][1000 genomes]
rs2584320	0.89[EUR][1000 genomes]
rs2584321	0.89[EUR][1000 genomes]
rs2584322	0.86[EUR][1000 genomes]
rs2584323	0.90[EUR][1000 genomes]
rs2584324	0.90[EUR][1000 genomes]
rs2584329	0.89[EUR][1000 genomes]
rs2790744	0.89[EUR][1000 genomes]
rs2790745	0.89[EUR][1000 genomes]
rs2790746	0.88[EUR][1000 genomes]
rs2790747	0.88[EUR][1000 genomes]
rs2790748	0.89[EUR][1000 genomes]
rs2800848	0.82[EUR][1000 genomes]
rs2800849	0.89[EUR][1000 genomes]
rs2800859	0.94[YRI][hapmap]
rs2800860	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[YRI][hapmap];0.94[ASN][1000 genomes]
rs2800861	0.88[EUR][1000 genomes]
rs2800865	0.89[EUR][1000 genomes]
rs2800866	0.89[EUR][1000 genomes]
rs2800867	0.89[EUR][1000 genomes]
rs2970199	0.91[ASN][1000 genomes]
rs3014719	0.86[EUR][1000 genomes]
rs56120858	0.94[EUR][1000 genomes]
rs61823931	0.89[EUR][1000 genomes]
rs6604697	0.86[EUR][1000 genomes]
rs6677832	0.94[EUR][1000 genomes]
rs7538392	0.91[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	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12139468	IARS2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222169200-222184000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:222182400-222184000	Enhancers	Osteobl	bone
3	chr1:222182800-222183800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr1:222183200-222185600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:222183200-222191400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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