Variant report

Variant	rs964424
Chromosome Location	chr15:39865699-39865700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39864644..39866716-chr15:39867291..39870082,2	MCF-7	breast:
2	chr15:39861270..39862826-chr15:39863131..39865842,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10152640	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10520137	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs10520138	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070220	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11070221	0.80[ASN][1000 genomes]
rs11070222	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs11070223	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11070224	0.80[ASN][1000 genomes]
rs11070225	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1134485	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1134486	0.85[ASN][1000 genomes]
rs11857819	0.81[ASN][1000 genomes]
rs12050804	0.80[TSI][hapmap]
rs12443011	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908846	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs12912082	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1478604	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1478605	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16969386	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs16969395	0.84[ASN][1000 genomes]
rs16969410	0.81[ASN][1000 genomes]
rs1876852	0.94[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1904209	0.87[ASN][1000 genomes]
rs2169830	0.83[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2228261	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2229364	0.85[ASN][1000 genomes]
rs2292305	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2411310	0.80[TSI][hapmap]
rs2411315	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2412412	0.94[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412418	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412419	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2412420	0.80[ASN][1000 genomes]
rs2618162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664139	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2664141	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743125	0.85[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs4319740	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56938133	0.80[ASN][1000 genomes]
rs66781090	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67239630	0.80[ASN][1000 genomes]
rs7167366	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7170682	0.91[ASN][1000 genomes]
rs7176721	0.82[AMR][1000 genomes]
rs7177324	0.82[ASN][1000 genomes]
rs7179293	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7183544	0.92[ASN][1000 genomes]
rs753598	0.85[ASN][1000 genomes]
rs753599	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8032035	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs8034594	0.94[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036376	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8036633	0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs8039035	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs949646	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs970280	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9806365	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806647	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs964424	CASC5	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39851000-39871800	Weak transcription	Pancreas	Pancrea
2	chr15:39854400-39870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39857800-39870600	Weak transcription	HSMMtube	muscle
4	chr15:39863600-39871200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:39865000-39865800	Enhancers	Colon Smooth Muscle	Colon
6	chr15:39865000-39865800	Enhancers	Esophagus	oesophagus
7	chr15:39865000-39866400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:39865200-39866800	Enhancers	Rectal Smooth Muscle	rectum
9	chr15:39865200-39867000	Enhancers	NHDF-Ad	bronchial
10	chr15:39865400-39866000	Enhancers	HepG2	liver
11	chr15:39865400-39866400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:39865400-39867000	Enhancers	Osteobl	bone
13	chr15:39865400-39867400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:39865600-39865800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr15:39865600-39866000	Enhancers	Adipose Nuclei	Adipose
16	chr15:39865600-39866000	Enhancers	Stomach Smooth Muscle	stomach
17	chr15:39865600-39866200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:39865600-39866200	Enhancers	Fetal Lung	lung
19	chr15:39865600-39866400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:39865600-39866600	Enhancers	Fetal Stomach	stomach
21	chr15:39865600-39867400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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