Variant report

Variant	rs10846557
Chromosome Location	chr12:124265053-124265054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10773036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10846554	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846558	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057352	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057353	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11057355	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11057357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057359	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834698	0.85[ASN][1000 genomes]
rs12099921	0.94[ASN][1000 genomes]
rs1568028	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2340692	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs36085880	0.88[ASN][1000 genomes]
rs56759847	0.91[ASN][1000 genomes]
rs59341883	0.91[ASN][1000 genomes]
rs61143657	0.88[ASN][1000 genomes]
rs7131750	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137310	0.83[EUR][1000 genomes]
rs7303002	0.84[EUR][1000 genomes]
rs7962448	0.94[ASN][1000 genomes]
rs7964186	0.85[ASN][1000 genomes]
rs7965847	1.00[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7978454	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9888323	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]

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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10846557	TCTN2	cis	cerebellum	SCAN
rs10846557	TCTN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124255600-124270800	Weak transcription	Brain Anterior Caudate	brain

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