Variant report

Variant	rs16866864
Chromosome Location	chr2:180488450-180488451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13391446	0.99[ASN][1000 genomes]
rs1515275	1.00[JPT][hapmap]
rs1588847	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs1588849	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs1588850	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2090219	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3106703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3106704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3106705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3106706	0.93[ASN][1000 genomes]
rs3112939	0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3112940	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112945	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs3112954	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3112955	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs3112958	0.99[ASN][1000 genomes]
rs3112959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[ASN][1000 genomes]
rs3112962	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs3112964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3112969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710552	0.91[ASN][1000 genomes]
rs6713726	0.93[ASN][1000 genomes]
rs9753151	0.95[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16866864	MTX2	cis	cerebellum	SCAN
rs16866864	NEUROD1	cis	parietal	SCAN
rs16866864	HOXD12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180486000-180494600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:180486400-180489800	Enhancers	Fetal Heart	heart
3	chr2:180487400-180489600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:180487800-180490800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:180488400-180494600	Weak transcription	Lung	lung

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