Variant report

Variant	rs7954182
Chromosome Location	chr12:68364283-68364284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYRK2-2	chr12:68363592-68364900	XLOC_009793
2	lnc-DYRK2-2	chr12:68363591-68364900	NONHSAT029273

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10735943	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs10748092	0.91[ASN][1000 genomes]
rs10784659	0.87[AFR][1000 genomes]
rs10784660	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784661	0.89[ASN][1000 genomes]
rs10784662	0.89[ASN][1000 genomes]
rs10784664	0.94[ASN][1000 genomes]
rs10878702	0.84[AFR][1000 genomes]
rs10878705	0.94[AFR][1000 genomes]
rs10878708	0.89[ASN][1000 genomes]
rs10878709	0.89[ASN][1000 genomes]
rs10878710	0.89[ASN][1000 genomes]
rs10878711	0.90[ASN][1000 genomes]
rs10878717	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878722	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11176965	0.84[AFR][1000 genomes]
rs11176970	0.89[ASN][1000 genomes]
rs11176971	0.89[ASN][1000 genomes]
rs11176976	0.91[ASN][1000 genomes]
rs11176977	0.91[ASN][1000 genomes]
rs12228138	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1548650	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548651	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548652	0.91[ASN][1000 genomes]
rs1548653	0.91[ASN][1000 genomes]
rs1860007	0.91[ASN][1000 genomes]
rs1905452	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2097999	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2190735	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839995	0.91[ASN][1000 genomes]
rs2870964	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141136	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4913266	0.87[AFR][1000 genomes]
rs4913386	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56229556	0.87[AFR][1000 genomes]
rs6581784	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310108	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312407	1.00[ASW][hapmap];0.95[LWK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes]
rs7959275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962230	0.91[ASN][1000 genomes]
rs7965959	0.89[ASN][1000 genomes]
rs7979547	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7980416	0.89[ASW][hapmap];0.93[LWK][hapmap];0.86[YRI][hapmap];0.87[AFR][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	esv3411149	chr12:68066948-68435533	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1039638	chr12:68293351-68399871	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7954182	AVPR1A	cis	cerebellum	SCAN
rs7954182	LRRC10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68356200-68370600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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