Variant report

Variant	rs494439
Chromosome Location	chr13:63735240-63735241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1097374	1.00[ASN][1000 genomes]
rs1333457	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512877	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604877	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182444	0.93[ASN][1000 genomes]
rs188481	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1913174	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298763	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298765	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298766	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298776	0.93[ASN][1000 genomes]
rs298781	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298782	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298784	1.00[ASN][1000 genomes]
rs298788	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298789	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298790	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs298852	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298853	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298855	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298870	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298871	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298875	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs298876	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298880	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298881	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298883	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs298884	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298886	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298892	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298894	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298895	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298898	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298899	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012179	1.00[ASN][1000 genomes]
rs3095589	0.93[ASN][1000 genomes]
rs3095590	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106412	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106417	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106418	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106423	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119942	0.86[ASN][1000 genomes]
rs3119944	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119947	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119953	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119954	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404075	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419967	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs435653	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs478952	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs482669	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506703	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs539957	0.93[ASN][1000 genomes]
rs576321	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613822	0.88[ASN][1000 genomes]
rs982160	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753514	chr13:63221699-63959299	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1054643	chr13:63501148-63755650	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv900274	chr13:63511841-63864603	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900275	chr13:63511841-63865669	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1039454	chr13:63545468-63826462	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv541798	chr13:63545468-63826462	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1045647	chr13:63545468-64082080	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv541799	chr13:63545468-64082080	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv900276	chr13:63638329-63784286	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv900277	chr13:63666149-63892905	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1052016	chr13:63704346-63826462	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv541800	chr13:63704346-63826462	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs494439	ZMAT2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:63735200-63735600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr13:63735200-63735600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:63735200-63736400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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