Variant report

Variant	rs1509460
Chromosome Location	chr5:42433819-42433820
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	chr5:42425732..42427236-chr5:42432145..42434745,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10064323	0.93[ASN][1000 genomes]
rs10941576	0.93[ASN][1000 genomes]
rs10941577	0.81[AMR][1000 genomes]
rs1117110	0.98[ASN][1000 genomes]
rs11738365	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11739243	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs11741390	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]
rs12513643	0.91[ASN][1000 genomes]
rs12514403	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12515480	0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12517368	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12517931	0.91[ASN][1000 genomes]
rs12518010	0.96[ASN][1000 genomes]
rs12518274	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12520318	0.91[ASN][1000 genomes]
rs12522222	0.96[ASN][1000 genomes]
rs12522421	0.96[ASN][1000 genomes]
rs12523537	0.93[ASN][1000 genomes]
rs12654242	0.89[ASN][1000 genomes]
rs13153388	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap]
rs13166285	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[AMR][1000 genomes]
rs13178282	0.81[AMR][1000 genomes]
rs13185872	0.93[ASN][1000 genomes]
rs13189275	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap]
rs1396768	0.98[ASN][1000 genomes]
rs1396775	0.93[ASN][1000 genomes]
rs1472947	0.93[ASN][1000 genomes]
rs1509455	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1509456	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1509462	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1605851	0.95[ASN][1000 genomes]
rs16872537	0.91[ASN][1000 genomes]
rs16872543	0.91[ASN][1000 genomes]
rs16872564	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1858136	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1858138	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876790	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1960498	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1979994	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2036745	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2202883	0.98[ASN][1000 genomes]
rs2221712	0.98[ASN][1000 genomes]
rs2395970	0.98[ASN][1000 genomes]
rs28498583	0.96[ASN][1000 genomes]
rs28943877	0.91[ASN][1000 genomes]
rs28943879	0.84[ASN][1000 genomes]
rs2940912	0.89[ASN][1000 genomes]
rs2940913	0.82[CEU][hapmap];0.83[CHB][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs2940914	0.98[ASN][1000 genomes]
rs2940917	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2940918	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2940919	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2940922	0.96[ASN][1000 genomes]
rs2940923	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940927	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2940934	0.98[ASN][1000 genomes]
rs2940940	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2940944	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs2940945	0.95[ASN][1000 genomes]
rs2972393	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap]
rs2972394	0.93[ASN][1000 genomes]
rs2972406	0.98[ASN][1000 genomes]
rs2972407	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2972408	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972410	0.96[ASN][1000 genomes]
rs2972411	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2972412	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2972413	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2972414	0.84[ASN][1000 genomes]
rs2972418	0.91[CHB][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap]
rs2972420	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs33956936	0.80[AMR][1000 genomes]
rs3764453	0.93[ASN][1000 genomes]
rs4130114	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs4358532	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4509029	0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.80[AMR][1000 genomes]
rs4530764	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap]
rs4866781	0.96[ASN][1000 genomes]
rs4866782	0.96[ASN][1000 genomes]
rs4866788	0.93[ASN][1000 genomes]
rs4866795	0.91[ASN][1000 genomes]
rs4866896	0.91[ASN][1000 genomes]
rs4866901	0.91[ASN][1000 genomes]
rs4866919	0.96[ASN][1000 genomes]
rs4866931	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs4866934	0.80[AMR][1000 genomes]
rs6451621	0.84[ASN][1000 genomes]
rs6451624	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs7721578	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs906817	0.95[ASN][1000 genomes]
rs9686537	0.93[ASN][1000 genomes]
rs9687863	0.89[ASN][1000 genomes]
rs979233	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs991592	0.93[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1509460	PCCB	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42425600-42434200	Weak transcription	Left Ventricle	heart
2	chr5:42426600-42435200	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:42426600-42436000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:42430600-42438800	Weak transcription	Aorta	Aorta
5	chr5:42430800-42434000	Weak transcription	Liver	Liver
6	chr5:42431800-42434800	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:42431800-42436000	Weak transcription	Fetal Lung	lung
8	chr5:42433000-42435400	Enhancers	Adipose Nuclei	Adipose
9	chr5:42433000-42437000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:42433600-42435000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:42433600-42436600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:42433600-42437000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:42433800-42434000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:42433800-42435000	Enhancers	Psoas Muscle	Psoas

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