Variant report

Variant	rs3731201
Chromosome Location	chr9:21988896-21988897
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	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
2	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229298	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10757262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1333034	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs1333035	0.89[CEU][hapmap]
rs17694493	1.00[CHB][hapmap]
rs2069422	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2069426	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2518721	0.88[ASN][1000 genomes]
rs2518722	1.00[JPT][hapmap]
rs2811709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2811712	0.89[CEU][hapmap]
rs3218018	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3731246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4977750	1.00[JPT][hapmap]
rs56018935	0.88[ASN][1000 genomes]
rs598664	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs662463	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3492902	chr9:21971026-22006145	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3492901	chr9:21971095-22006263	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3731201	CDKN2B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21987000-21989400	Active TSS	NHDF-Ad	bronchial
2	chr9:21987200-21992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:21987400-21989000	Enhancers	GM12878-XiMat	blood
4	chr9:21988000-21989600	Weak transcription	HSMM	muscle
5	chr9:21988000-21993000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:21988200-21989000	Flanking Active TSS	Hela-S3	cervix
7	chr9:21988200-21990000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:21988400-21989000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:21988400-21989000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:21988400-21989200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:21988400-21990800	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr9:21988600-21989000	Flanking Active TSS	NHEK	skin
13	chr9:21988600-21989000	Active TSS	Osteobl	bone
14	chr9:21988600-21989200	Weak transcription	NH-A	brain
15	chr9:21988600-21989400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:21988600-21989400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:21988800-21989000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:21988800-21989000	Enhancers	HMEC	breast
19	chr9:21988800-21989000	Flanking Active TSS	NHLF	lung
20	chr9:21988800-21989400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:21988800-21989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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