Variant report

Variant	rs2217989
Chromosome Location	chr18:28742058-28742059
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10502560	0.86[CHB][hapmap]
rs10853409	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11081681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11874325	0.87[CHB][hapmap]
rs11877142	0.87[CHB][hapmap]
rs11877211	0.86[CHB][hapmap]
rs12455973	0.87[CHB][hapmap]
rs12458919	0.85[CHB][hapmap]
rs12606879	0.87[CHB][hapmap]
rs12606918	0.87[CHB][hapmap]
rs12608367	0.87[CHB][hapmap]
rs1437605	0.80[EUR][1000 genomes]
rs1437606	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1982161	0.84[CHB][hapmap]
rs1982162	0.86[CHB][hapmap]
rs2246736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577064	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577072	0.85[CHB][hapmap]
rs2577074	0.87[CHB][hapmap]
rs2577075	0.87[CHB][hapmap]
rs2851999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852000	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786169	0.87[CHB][hapmap]
rs6506884	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506887	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6506889	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506890	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506891	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506894	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7238483	0.87[CHB][hapmap]
rs7244982	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7245164	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245261	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097223	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9956307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv132191	chr18:28739028-28745912	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv131242	chr18:28739028-28748058	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2217989	FAM59A	cis	cerebellum	SCAN
rs2217989	DSC1	cis	parietal	SCAN
rs2217989	AQP4	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28730600-28742600	Weak transcription	Esophagus	oesophagus
2	chr18:28737400-28746400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr18:28737600-28742200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:28737600-28742200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr18:28737600-28742400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr18:28738000-28742200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:28741400-28742200	Enhancers	HMEC	breast
8	chr18:28741400-28742200	Enhancers	NHEK	skin
9	chr18:28741400-28742800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr18:28741400-28743200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:28741400-28743200	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr18:28741400-28743200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr18:28742000-28742200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:28742000-28742400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr18:28742000-28742600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr18:28742000-28742600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr18:28742000-28742600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr18:28742000-28742800	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr18:28742000-28743000	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr18:28742000-28743000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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