Variant report

Variant	rs1040756
Chromosome Location	chr20:13652982-13652983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13652495..13656691-chr20:13764074..13766067,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11087055	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11087056	0.94[EUR][1000 genomes]
rs13040087	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2057259	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2180569	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2295503	0.87[ASN][1000 genomes]
rs2295504	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs2327793	0.93[ASN][1000 genomes]
rs2423732	0.88[ASN][1000 genomes]
rs2423733	0.90[ASN][1000 genomes]
rs2423734	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2423736	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2423737	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2423738	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2423739	0.92[ASN][1000 genomes]
rs34146992	0.86[ASN][1000 genomes]
rs34822601	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4303776	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4441543	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033766	0.86[ASN][1000 genomes]
rs6033767	0.88[ASN][1000 genomes]
rs6033768	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs6033783	0.88[ASN][1000 genomes]
rs6033793	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6033795	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042225	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6042236	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6042239	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6042240	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6042264	0.86[ASN][1000 genomes]
rs6042273	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6042285	0.94[ASN][1000 genomes]
rs6042301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042304	0.95[EUR][1000 genomes]
rs6105137	0.88[ASN][1000 genomes]
rs6109983	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs6109990	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6109993	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109995	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6131499	0.91[ASN][1000 genomes]
rs6134919	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6134930	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6134935	0.86[ASN][1000 genomes]
rs6134948	0.89[ASN][1000 genomes]
rs6514418	0.84[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1040756	PCSK2	cis	cerebellum	SCAN
rs1040756	MKKS	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13649400-13653600	Enhancers	Dnd41	blood
2	chr20:13651000-13653000	Enhancers	Thymus	Thymus
3	chr20:13651000-13653200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:13651400-13653600	Enhancers	Fetal Lung	lung
5	chr20:13651600-13654200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr20:13651800-13653600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:13651800-13654000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:13651800-13654000	Enhancers	Osteobl	bone
9	chr20:13652200-13653600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr20:13652400-13653200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:13652400-13653200	Weak transcription	Aorta	Aorta
12	chr20:13652400-13653400	Enhancers	HSMM	muscle
13	chr20:13652600-13653000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:13652800-13653600	Enhancers	Adipose Nuclei	Adipose
15	chr20:13652800-13653800	Enhancers	Liver	Liver
16	chr20:13652800-13656800	Weak transcription	Fetal Stomach	stomach

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