Variant report

Variant	rs1109557
Chromosome Location	chr20:23312525-23312526
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	chr20:23311621..23313833-chr20:23315735..23318823,3	MCF-7	breast:
2	chr20:23311600..23313681-chr20:23341000..23343675,2	K562	blood:

Variant related genes	Relation type
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10485644	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1122407	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs12625187	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12625257	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs12625297	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12625489	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12625948	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12625994	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs16985266	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs16985303	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16985337	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs2236024	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs34036626	0.94[AMR][1000 genomes]
rs34831633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736756	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes]
rs3761276	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3761278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57034369	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57322153	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57436024	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57535381	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58192622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59143301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048853	1.00[CEU][hapmap]
rs6048856	1.00[CEU][hapmap]
rs61024391	0.89[AMR][1000 genomes]
rs6114159	1.00[CEU][hapmap]
rs6114160	1.00[CEU][hapmap]
rs61297472	0.89[AMR][1000 genomes]
rs61344818	0.94[AMR][1000 genomes]
rs7265627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7266535	1.00[CEU][hapmap]
rs73901859	0.89[AMR][1000 genomes]
rs8115832	0.89[AMR][1000 genomes]
rs8123389	0.84[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1109557	CST3	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23307800-23314800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr20:23311800-23315000	Enhancers	K562	blood
3	chr20:23312000-23312600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:23312200-23313200	Enhancers	HUVEC	blood vessel
5	chr20:23312400-23313400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:23312400-23313400	Enhancers	GM12878-XiMat	blood
7	chr20:23312400-23317600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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