Variant report

Variant	rs2340692
Chromosome Location	chr12:124268281-124268282
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	chr12:124267933..124270211-chr12:124272777..124275350,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1022320	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1022321	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs1050448	1.00[CHB][hapmap]
rs10744163	1.00[CHB][hapmap]
rs10773036	0.88[CEU][hapmap]
rs10846554	0.82[EUR][1000 genomes]
rs10846556	1.00[ASN][1000 genomes]
rs10846557	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10846558	0.84[EUR][1000 genomes]
rs10846559	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs10846569	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11057352	0.82[EUR][1000 genomes]
rs11057355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057357	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11057358	1.00[ASN][1000 genomes]
rs11057359	0.83[EUR][1000 genomes]
rs1114628	1.00[CHB][hapmap]
rs11832329	1.00[ASN][1000 genomes]
rs11835233	1.00[ASN][1000 genomes]
rs11835252	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs12302651	0.83[CEU][hapmap]
rs12809853	1.00[CHB][hapmap]
rs15587	1.00[CHB][hapmap]
rs1568027	1.00[ASN][1000 genomes]
rs1568028	0.83[EUR][1000 genomes]
rs1568029	1.00[ASN][1000 genomes]
rs1568030	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs2674504	1.00[ASN][1000 genomes]
rs2674506	1.00[ASN][1000 genomes]
rs3204541	1.00[CHB][hapmap]
rs34506612	1.00[ASN][1000 genomes]
rs34535130	1.00[ASN][1000 genomes]
rs34705855	1.00[ASN][1000 genomes]
rs4930728	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4930732	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55920625	1.00[ASN][1000 genomes]
rs56399357	1.00[ASN][1000 genomes]
rs61953572	1.00[ASN][1000 genomes]
rs67861770	1.00[ASN][1000 genomes]
rs7131750	0.82[EUR][1000 genomes]
rs7136121	1.00[ASN][1000 genomes]
rs7137299	1.00[ASN][1000 genomes]
rs7137310	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458816	1.00[ASN][1000 genomes]
rs7303002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9888323	0.84[CEU][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
rs2340692	TCTN2	cis	parietal	SCAN
rs2340692	TCTN2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124255600-124270800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:124265800-124275200	Weak transcription	Fetal Brain Female	brain
3	chr12:124266000-124269400	Weak transcription	Fetal Brain Male	brain

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