Variant report

Variant	rs2898044
Chromosome Location	chr5:126811978-126811979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10519936	0.93[CEU][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs10519937	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10519938	0.93[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs11743934	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11949330	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11949373	0.84[EUR][1000 genomes]
rs11950058	0.84[EUR][1000 genomes]
rs11950427	0.93[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11952366	0.89[EUR][1000 genomes]
rs11952552	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs11952947	0.84[EUR][1000 genomes]
rs11953024	0.84[EUR][1000 genomes]
rs11958435	0.84[EUR][1000 genomes]
rs11959505	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs12233927	0.93[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12234066	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1363385	0.85[EUR][1000 genomes]
rs1363388	0.93[CEU][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap]
rs1363631	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1422318	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1529467	0.84[EUR][1000 genomes]
rs1593949	0.89[EUR][1000 genomes]
rs1593950	0.89[EUR][1000 genomes]
rs17164902	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17164903	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17164915	0.89[EUR][1000 genomes]
rs17164935	0.81[TSI][hapmap]
rs17164979	0.84[EUR][1000 genomes]
rs17164996	0.93[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17165090	0.93[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs173509	0.82[EUR][1000 genomes]
rs17604615	0.88[TSI][hapmap]
rs17604889	0.81[TSI][hapmap]
rs17673685	0.81[TSI][hapmap]
rs17839690	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17839693	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs17839695	0.85[EUR][1000 genomes]
rs2173978	0.89[EUR][1000 genomes]
rs2408871	0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2408873	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2434620	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3756721	0.93[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs3812054	0.88[TSI][hapmap]
rs3812055	0.93[CHD][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs3844184	0.93[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs3851469	0.93[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs3909351	0.93[CEU][hapmap]
rs4395678	0.91[EUR][1000 genomes]
rs4563674	0.84[EUR][1000 genomes]
rs4604231	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4637594	0.89[EUR][1000 genomes]
rs55663031	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55763657	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56006993	0.82[EUR][1000 genomes]
rs57411417	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59745967	0.87[EUR][1000 genomes]
rs60153933	0.87[EUR][1000 genomes]
rs60901740	0.87[EUR][1000 genomes]
rs61175766	0.88[EUR][1000 genomes]
rs6595764	0.85[EUR][1000 genomes]
rs6595767	0.93[CHD][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs6595768	0.88[TSI][hapmap]
rs6595769	0.93[CHD][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs67200948	0.83[EUR][1000 genomes]
rs67425941	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67854568	0.84[EUR][1000 genomes]
rs68035691	0.84[EUR][1000 genomes]
rs6874392	0.84[EUR][1000 genomes]
rs6874752	0.84[EUR][1000 genomes]
rs6881894	0.93[CEU][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs6888010	0.85[EUR][1000 genomes]
rs6891785	0.84[EUR][1000 genomes]
rs6897290	0.81[EUR][1000 genomes]
rs72790422	0.84[EUR][1000 genomes]
rs72790424	0.84[EUR][1000 genomes]
rs72790426	0.84[EUR][1000 genomes]
rs7700469	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2898044	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:126811600-126812000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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