Variant report

Variant	rs10152903
Chromosome Location	chr15:39798639-39798640
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	chr15:39796929..39799190-chr15:39801226..39804372,3	MCF-7	breast:
2	chr15:39798382..39801235-chr15:39873000..39875573,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10152951	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1038097	1.00[ASN][1000 genomes]
rs1051442	1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs10520141	1.00[CHB][hapmap]
rs10520143	1.00[CHB][hapmap]
rs10520146	1.00[CHB][hapmap]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap]
rs1159994	0.84[TSI][hapmap]
rs12438058	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12442155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379938	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1382443	1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs1382444	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs1478606	0.84[TSI][hapmap]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969487	1.00[CHB][hapmap]
rs16969491	1.00[CHB][hapmap]
rs16969547	1.00[CHB][hapmap]
rs17631807	1.00[ASN][1000 genomes]
rs17633107	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17633210	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17702987	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705806	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17706083	1.00[CHB][hapmap]
rs17706179	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1813493	1.00[ASN][1000 genomes]
rs1947783	0.84[TSI][hapmap]
rs1994380	1.00[CHB][hapmap]
rs2129457	1.00[CHB][hapmap]
rs2228262	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2228263	1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs2411292	0.84[TSI][hapmap]
rs2411316	1.00[CHB][hapmap]
rs2618156	1.00[ASN][1000 genomes]
rs2618161	1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2664123	1.00[ASN][1000 genomes]
rs2664137	1.00[ASN][1000 genomes]
rs2664138	1.00[CHB][hapmap]
rs28622135	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	1.00[ASN][1000 genomes]
rs4415979	1.00[CHB][hapmap]
rs4503768	1.00[CHB][hapmap]
rs4923835	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs58188999	1.00[ASN][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002378	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002379	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002380	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002384	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492905	1.00[CHB][hapmap]
rs7179604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008526	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008647	1.00[ASN][1000 genomes]
rs880270	1.00[CHB][hapmap]
rs9972350	1.00[CHB][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10152903	CENPL	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39789000-39800800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:39789000-39803200	Weak transcription	Left Ventricle	heart
3	chr15:39791600-39803200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:39791600-39803400	Weak transcription	Fetal Lung	lung
5	chr15:39792200-39803600	Weak transcription	Ovary	ovary
6	chr15:39793800-39802200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:39793800-39803200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:39793800-39803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:39794000-39800600	Weak transcription	HSMM	muscle
10	chr15:39794400-39802800	Weak transcription	Fetal Heart	heart
11	chr15:39794600-39801000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:39795400-39800600	Weak transcription	K562	blood
13	chr15:39795400-39803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:39795800-39799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:39796200-39799600	Enhancers	Osteobl	bone
16	chr15:39796400-39799400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:39796600-39799200	Enhancers	NH-A	brain
18	chr15:39796800-39804000	Weak transcription	Lung	lung
19	chr15:39797000-39803200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:39797200-39798800	Weak transcription	HMEC	breast
21	chr15:39797600-39800800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:39797600-39800800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:39797600-39803200	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:39797800-39800800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:39798000-39802400	Weak transcription	NHDF-Ad	bronchial
26	chr15:39798400-39803200	Weak transcription	NHLF	lung
27	chr15:39798600-39799200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:39798600-39799400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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