Variant report

Variant	rs1116547
Chromosome Location	chr5:112680337-112680338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10042223	0.88[YRI][hapmap]
rs10051834	0.91[YRI][hapmap]
rs10062004	0.87[YRI][hapmap]
rs10074214	0.88[YRI][hapmap]
rs10077020	0.86[ASN][1000 genomes]
rs10428666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10519343	0.95[MEX][hapmap]
rs10519346	0.95[MEX][hapmap]
rs10900685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11241201	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241209	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11738075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740353	0.95[MEX][hapmap]
rs11741916	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741963	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11743052	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11744606	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11746821	0.85[EUR][1000 genomes]
rs11747924	0.84[JPT][hapmap]
rs11748465	0.95[MEX][hapmap]
rs11748503	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11748524	0.95[MEX][hapmap]
rs11750945	0.91[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12152879	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188069	0.90[MEX][hapmap]
rs12514091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12516418	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12518849	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12519753	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12520003	1.00[CHB][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12521391	0.90[MEX][hapmap]
rs12522862	0.90[MEX][hapmap]
rs12523255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188946	0.88[YRI][hapmap]
rs13360719	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1366393	0.88[YRI][hapmap]
rs1443683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1517209	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586943	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135463	0.90[MEX][hapmap]
rs17135488	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs17135515	0.95[MEX][hapmap]
rs17135526	0.95[MEX][hapmap]
rs17135534	0.86[MEX][hapmap]
rs17135597	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17135630	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1833678	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1838208	0.86[ASN][1000 genomes]
rs1850407	0.88[YRI][hapmap]
rs1850410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1850412	0.88[YRI][hapmap]
rs1965429	0.82[YRI][hapmap]
rs1997521	0.92[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2042222	0.88[JPT][hapmap]
rs2068923	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2091803	0.82[MEX][hapmap]
rs2222144	0.88[YRI][hapmap]
rs26959	0.92[YRI][hapmap]
rs26961	0.91[YRI][hapmap]
rs26966	0.91[YRI][hapmap]
rs27567	0.92[YRI][hapmap]
rs3846721	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3846722	0.88[JPT][hapmap]
rs4331889	0.92[YRI][hapmap]
rs4705551	0.88[JPT][hapmap]
rs4705806	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4705807	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4705808	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4705809	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4705814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705817	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705818	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705819	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705826	1.00[JPT][hapmap]
rs56362568	0.81[EUR][1000 genomes]
rs59107004	0.84[EUR][1000 genomes]
rs59222257	0.84[EUR][1000 genomes]
rs59954246	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60087454	0.84[EUR][1000 genomes]
rs62374372	0.94[ASN][1000 genomes]
rs6594701	1.00[YRI][hapmap]
rs6594703	0.95[YRI][hapmap]
rs6594704	0.92[YRI][hapmap]
rs6594705	0.92[YRI][hapmap]
rs6594707	0.84[YRI][hapmap]
rs6594710	0.88[YRI][hapmap]
rs6594712	0.88[YRI][hapmap]
rs66502937	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66583752	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66644309	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66728961	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66893265	0.84[EUR][1000 genomes]
rs67063423	0.84[EUR][1000 genomes]
rs67268709	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67303814	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67373655	0.84[EUR][1000 genomes]
rs67550282	0.84[EUR][1000 genomes]
rs67764628	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68069850	0.83[EUR][1000 genomes]
rs6861786	0.86[ASN][1000 genomes]
rs6864528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6867397	0.88[YRI][hapmap]
rs6877524	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6878001	0.88[JPT][hapmap];0.81[MEX][hapmap]
rs6879800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6882900	0.86[ASN][1000 genomes]
rs6883441	0.88[JPT][hapmap]
rs6887565	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs6888602	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6894687	0.84[YRI][hapmap]
rs72792179	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73236478	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73236479	0.94[ASN][1000 genomes]
rs73244779	0.83[EUR][1000 genomes]
rs7707443	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7708084	0.85[YRI][hapmap]
rs7717000	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7717422	0.88[YRI][hapmap]
rs7724707	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7724717	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7724936	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7725589	0.91[YRI][hapmap]
rs9326886	0.87[YRI][hapmap]
rs9326887	0.90[YRI][hapmap]
rs9326888	0.88[YRI][hapmap]
rs957777	1.00[JPT][hapmap]
rs9632462	0.84[YRI][hapmap]
rs971370	0.86[MEX][hapmap]
rs971371	0.86[MEX][hapmap]
rs977997	0.86[MEX][hapmap]
rs9800316	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cerebral amyloid angiopathy	25188341	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1116547	YTHDC2	cis	cerebellum	SCAN
rs1116547	MCC	cis	parietal	SCAN
rs1116547	DCP2	cis	parietal	SCAN
rs1116547	YTHDC2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112667000-112681000	Weak transcription	Esophagus	oesophagus
2	chr5:112667200-112680400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112667200-112680600	Weak transcription	NHEK	skin
4	chr5:112667200-112680800	Weak transcription	Right Ventricle	heart
5	chr5:112667200-112681000	Weak transcription	Pancreas	Pancrea
6	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112678800-112681400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:112678800-112681600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:112678800-112682400	Enhancers	HMEC	breast
10	chr5:112679000-112682000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:112679400-112680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:112679400-112681000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:112679400-112681400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:112679800-112680800	Weak transcription	Fetal Heart	heart
15	chr5:112679800-112683000	Weak transcription	Fetal Stomach	stomach

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