Variant report

Variant	rs852251
Chromosome Location	chr5:35922462-35922463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:35651056..35651909-chr5:35922306..35923146,4	MCF-7	breast:
2	chr5:35651061..35651901-chr5:35922282..35923222,3	MCF-7	breast:
3	chr5:35918022..35920429-chr5:35920583..35922848,2	MCF-7	breast:
4	chr5:35777376..35779167-chr5:35921282..35923743,2	MCF-7	breast:
5	chr5:35777408..35778477-chr5:35922335..35923637,7	MCF-7	breast:
6	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10063445	0.91[JPT][hapmap]
rs10074095	0.91[JPT][hapmap]
rs10074127	0.91[JPT][hapmap]
rs10461959	0.91[JPT][hapmap]
rs10491432	0.83[AFR][1000 genomes]
rs10491433	0.83[AFR][1000 genomes]
rs10941267	0.91[JPT][hapmap]
rs11567762	0.83[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs12055232	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516866	0.90[JPT][hapmap]
rs1353251	0.91[JPT][hapmap]
rs1389830	0.91[JPT][hapmap]
rs1423657	0.80[EUR][1000 genomes]
rs1423658	0.80[EUR][1000 genomes]
rs1494555	0.91[JPT][hapmap]
rs1494556	0.91[JPT][hapmap]
rs1494567	0.81[JPT][hapmap]
rs16902557	0.83[AFR][1000 genomes]
rs16902562	0.83[AFR][1000 genomes]
rs16902592	0.89[AFR][1000 genomes]
rs16902593	0.89[AFR][1000 genomes]
rs16902594	0.89[AFR][1000 genomes]
rs3777090	0.91[JPT][hapmap]
rs4141646	0.80[EUR][1000 genomes]
rs57498894	0.89[AFR][1000 genomes]
rs6862142	0.86[JPT][hapmap]
rs6870944	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6893142	0.91[JPT][hapmap]
rs73094019	0.83[AFR][1000 genomes]
rs73094022	0.83[AFR][1000 genomes]
rs7716064	0.91[JPT][hapmap]
rs7724777	0.84[AFR][1000 genomes]
rs852244	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs852246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852249	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs852250	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs852252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs852253	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860416	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs863781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292616	0.91[JPT][hapmap]
rs9292617	0.91[JPT][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	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv4794	chr5:35906690-35934205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs852251	CDKN2B	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35915600-35924200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:35919600-35924200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:35920000-35923400	Weak transcription	Osteobl	bone
4	chr5:35920000-35924000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:35920000-35924200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:35920000-35924600	Weak transcription	HSMMtube	muscle
7	chr5:35920200-35923400	Weak transcription	NHDF-Ad	bronchial
8	chr5:35920200-35923600	Weak transcription	HMEC	breast
9	chr5:35920200-35924000	Weak transcription	Hela-S3	cervix
10	chr5:35920400-35923200	Weak transcription	NHLF	lung
11	chr5:35920400-35924000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:35920400-35924200	Weak transcription	NHEK	skin
13	chr5:35920600-35924200	Enhancers	Dnd41	blood
14	chr5:35920600-35924400	Enhancers	Thymus	Thymus
15	chr5:35920800-35923600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:35920800-35924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:35920800-35924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:35921000-35922800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:35921000-35924200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:35921600-35923400	Enhancers	Fetal Thymus	thymus

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