Variant report

Variant	rs1158167
Chromosome Location	chr20:23578189-23578190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23575532..23578369-chr20:23585910..23588143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173335	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1010117	0.86[EUR][1000 genomes]
rs1011226	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs12624424	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12625182	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12625716	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs12710327	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13037490	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038305	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs13038337	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13038990	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13039536	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs13040663	0.82[EUR][1000 genomes]
rs13041070	0.80[EUR][1000 genomes]
rs13043266	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043610	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1555355	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17751897	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2016161	0.80[EUR][1000 genomes]
rs2067488	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2208289	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254635	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs2405367	0.80[CEU][hapmap]
rs2405392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2405393	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424582	0.80[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs28703706	0.89[EUR][1000 genomes]
rs3004139	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004145	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088162	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs34374560	0.86[EUR][1000 genomes]
rs34746357	0.80[EUR][1000 genomes]
rs34792920	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897231	0.80[EUR][1000 genomes]
rs34911568	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35488434	0.80[EUR][1000 genomes]
rs35573837	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35610040	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs35782710	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35966482	0.80[EUR][1000 genomes]
rs3761280	0.80[EUR][1000 genomes]
rs3761281	0.80[EUR][1000 genomes]
rs3787498	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3787499	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3810575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827141	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3827142	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs3827143	0.85[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs4346460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4815222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815223	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815224	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55897275	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56077567	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56371840	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56388902	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57549987	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59059917	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036463	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036465	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6036469	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036470	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036471	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036474	0.89[EUR][1000 genomes]
rs6036476	0.86[EUR][1000 genomes]
rs6036478	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6048920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048922	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048923	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048924	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048925	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048926	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048928	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048929	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048930	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6048933	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048936	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048937	0.82[EUR][1000 genomes]
rs6048939	0.86[EUR][1000 genomes]
rs6048941	0.88[EUR][1000 genomes]
rs6048945	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048946	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048949	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048950	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048952	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6048956	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs61035931	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6106685	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114201	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs6114206	0.86[EUR][1000 genomes]
rs6114208	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs6515375	0.81[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs67567111	0.80[EUR][1000 genomes]
rs67997662	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7265178	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7270413	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs734801	0.84[EUR][1000 genomes]
rs8114619	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8115417	0.89[EUR][1000 genomes]
rs8115423	0.89[EUR][1000 genomes]
rs8116859	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8121147	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8121283	0.89[EUR][1000 genomes]
rs8121405	0.89[EUR][1000 genomes]
rs911119	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cystatin C	17903292	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1158167	CST3	cis	cerebellum	SCAN
rs1158167	GINS1	cis	parietal	SCAN
rs1158167	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs1158167	CST3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23576800-23578800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr20:23577000-23578200	Enhancers	HMEC	breast
3	chr20:23577200-23578400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:23577400-23578200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:23578000-23578600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
6	chr20:23578000-23579200	Enhancers	Primary monocytes fromperipheralblood	blood

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