Variant report

Variant	rs12050804
Chromosome Location	chr15:39955786-39955787
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39926150..39927736-chr15:39954644..39957261,2	MCF-7	breast:
2	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
3	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
4	chr15:39876509..39878370-chr15:39955744..39957926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10152640	0.84[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10520138	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs10520142	0.84[YRI][hapmap]
rs1105159	0.91[CHB][hapmap]
rs11070231	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11631820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443011	0.84[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12899323	0.94[ASN][1000 genomes]
rs12900024	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12900583	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901142	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12903514	0.95[ASN][1000 genomes]
rs12911549	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12911999	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1478604	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs1876852	0.84[CEU][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs1906152	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1906155	0.87[ASN][1000 genomes]
rs1906156	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1994379	0.86[CHB][hapmap]
rs2129459	0.87[ASN][1000 genomes]
rs2169830	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs2411299	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2411300	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2411301	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2411304	0.83[ASN][1000 genomes]
rs2411307	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411308	0.94[ASN][1000 genomes]
rs2411309	0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411310	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411311	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411315	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs2412412	0.84[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2412418	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs2618163	0.94[CEU][hapmap]
rs2631697	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631700	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2631701	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631702	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631704	0.92[ASN][1000 genomes]
rs2631705	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2631710	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2664125	0.92[ASN][1000 genomes]
rs2664133	0.87[ASN][1000 genomes]
rs2664135	0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28437905	0.95[ASN][1000 genomes]
rs28581473	0.99[ASN][1000 genomes]
rs2898685	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3103065	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4319738	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319740	0.90[EUR][1000 genomes]
rs4429263	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4476148	0.94[ASN][1000 genomes]
rs4480779	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4493017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4572354	0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4591113	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4606692	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4924376	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4924377	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492909	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6492910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6492911	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs66781090	0.89[EUR][1000 genomes]
rs68183224	0.88[ASN][1000 genomes]
rs7167100	0.95[ASN][1000 genomes]
rs7167366	0.86[EUR][1000 genomes]
rs7170335	0.86[YRI][hapmap]
rs7177857	0.87[ASN][1000 genomes]
rs7179013	0.95[CHB][hapmap]
rs7179293	0.84[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs8033902	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs8034543	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8034594	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs8034885	0.94[ASN][1000 genomes]
rs8035354	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036226	0.95[ASN][1000 genomes]
rs8039035	0.86[EUR][1000 genomes]
rs8042068	0.94[ASN][1000 genomes]
rs937960	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs949646	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs951358	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9672572	0.89[ASN][1000 genomes]
rs9806365	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12050804	CASC5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39948400-39956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:39949400-39956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:39950200-39957200	Weak transcription	HSMM	muscle
5	chr15:39950400-39955800	Weak transcription	Hela-S3	cervix
6	chr15:39950400-39957200	Weak transcription	HSMMtube	muscle
7	chr15:39950800-39957800	Weak transcription	HUVEC	blood vessel
8	chr15:39954200-39955800	Weak transcription	NHLF	lung
9	chr15:39954400-39956400	Weak transcription	Fetal Kidney	kidney
10	chr15:39954400-39958200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:39954400-39958200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:39954400-39958200	Weak transcription	NH-A	brain
13	chr15:39954400-39959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:39954600-39958200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:39954800-39956200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:39955600-39956200	Enhancers	Fetal Lung	lung
17	chr15:39955600-39956400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:39955600-39959800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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