Variant report

Variant	rs6049760
Chromosome Location	chr20:24513596-24513597
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	chr20:24511434..24514163-chr20:24516038..24517958,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13041310	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1555892	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2386954	0.80[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2386956	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4283490	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036832	0.89[CEU][hapmap];0.81[MEX][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6049755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6049757	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6049758	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6049759	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6049765	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049768	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049771	0.89[CEU][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049775	1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6076233	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6076235	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6114752	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6114757	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6114760	0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6114768	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132742	0.89[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132743	0.89[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138316	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6049760	CST5	cis	parietal	SCAN
rs6049760	CST9	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24504000-24525800	Weak transcription	Aorta	Aorta
2	chr20:24508200-24523800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24510000-24515000	Weak transcription	Brain Substantia Nigra	brain
4	chr20:24510200-24515000	Weak transcription	Brain Hippocampus Middle	brain
5	chr20:24510800-24514400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:24510800-24518000	Weak transcription	Gastric	stomach
7	chr20:24510800-24525200	Weak transcription	Left Ventricle	heart
8	chr20:24511200-24513800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:24511400-24515800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:24511400-24516200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:24512600-24514200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr20:24513000-24515400	Weak transcription	Brain Angular Gyrus	brain
13	chr20:24513200-24516600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:24513400-24513600	Enhancers	Brain Anterior Caudate	brain

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