Variant report

Variant	rs10908813
Chromosome Location	chr1:160895847-160895848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10797087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10797089	0.86[EUR][1000 genomes]
rs10908809	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908810	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908811	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908812	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1092415	0.90[ASN][1000 genomes]
rs11265510	0.96[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11265514	0.90[EUR][1000 genomes]
rs11265516	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11265519	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11587040	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080285	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125065	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126310	0.85[MEX][hapmap]
rs12135639	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12740520	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810924	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1855186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1855187	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1930596	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1930598	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039415	0.88[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap]
rs2184064	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2225591	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2236515	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs2274905	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs2274907	0.84[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2274908	0.84[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2274910	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs34295669	0.87[EUR][1000 genomes]
rs3766356	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs3820094	0.84[CEU][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs3829790	0.81[MEX][hapmap]
rs3953093	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3953095	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4017453	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4129196	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656277	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656282	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656956	0.84[CEU][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs4656957	0.84[CEU][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs4656958	0.88[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap]
rs4656959	0.87[EUR][1000 genomes]
rs4656964	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656971	0.81[MEX][hapmap]
rs6427552	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs6427559	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6674437	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6691868	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6694415	0.85[EUR][1000 genomes]
rs6694743	0.84[EUR][1000 genomes]
rs6704490	0.85[EUR][1000 genomes]
rs7411035	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs7414826	0.88[EUR][1000 genomes]
rs7516660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7532133	0.83[JPT][hapmap]
rs7551697	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv947200	chr1:160870136-160905390	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10908813	LMNA	cis	parietal	SCAN
rs10908813	APCS	cis	cerebellum	SCAN
rs10908813	SPTA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160895000-160896000	Enhancers	Stomach Mucosa	stomach
2	chr1:160895200-160896000	Enhancers	Fetal Intestine Small	intestine
3	chr1:160895800-160896400	Enhancers	Duodenum Mucosa	Duodenum

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