Variant report

Variant	rs17405097
Chromosome Location	chr1:86465839-86465840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10873740	0.87[MEX][hapmap]
rs10873744	0.86[TSI][hapmap]
rs11161713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161714	0.87[MEX][hapmap]
rs11161717	0.87[MEX][hapmap]
rs11161734	0.89[TSI][hapmap]
rs12023979	0.81[EUR][1000 genomes]
rs12040977	0.81[EUR][1000 genomes]
rs12040981	0.81[EUR][1000 genomes]
rs12043664	0.80[EUR][1000 genomes]
rs12118004	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12125053	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12134342	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs489385	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs498554	0.82[EUR][1000 genomes]
rs516213	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs535637	1.00[ASW][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs569419	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs583315	0.86[ASW][hapmap];0.85[CHD][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs585708	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs613060	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61802174	0.80[EUR][1000 genomes]
rs640303	0.83[EUR][1000 genomes]
rs648833	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs662369	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6672107	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs7537787	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997110	0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1012808	chr1:86455710-86470489	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17405097	SYDE2	cis	parietal	SCAN
rs17405097	COL24A1	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86459200-86472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:86459200-86472200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86464000-86469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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