Variant report

Variant	rs662463
Chromosome Location	chr9:22030438-22030439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:22006840..22009770-chr9:22030122..22031727,2	MCF-7	breast:
2	chr9:22006075..22010521-chr9:22028543..22032768,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10757262	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11515	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs1333034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1333035	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17694493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs17694555	0.83[EUR][1000 genomes]
rs17694572	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17756311	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2069422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069426	1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2811712	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs3218018	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731201	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3731246	1.00[CHB][hapmap]
rs598664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974336	1.00[MEX][hapmap];0.86[TSI][hapmap]

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	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	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs662463	CDKN2B	cis	Whole Blood	GTEx
rs662463	CDKN2B	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22009800-22037000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:22022800-22032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:22025000-22033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:22025400-22039800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:22029000-22032400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr9:22029200-22031800	Strong transcription	Dnd41	blood
7	chr9:22029400-22030600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:22029400-22030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:22029400-22030800	Enhancers	NHDF-Ad	bronchial
10	chr9:22029400-22031000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr9:22029400-22031000	Enhancers	Hela-S3	cervix
12	chr9:22029400-22031000	Enhancers	HUVEC	blood vessel
13	chr9:22029400-22032600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:22029400-22034200	Enhancers	HMEC	breast
15	chr9:22029800-22031000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:22030000-22030600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:22030000-22030600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:22030000-22030600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:22030000-22030600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr9:22030000-22030600	Enhancers	Duodenum Mucosa	Duodenum
21	chr9:22030000-22030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:22030000-22030800	Enhancers	Fetal Intestine Small	intestine
23	chr9:22030000-22030800	Enhancers	GM12878-XiMat	blood
24	chr9:22030000-22030800	Enhancers	NH-A	brain
25	chr9:22030000-22030800	Enhancers	Osteobl	bone
26	chr9:22030000-22031000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:22030000-22034200	Enhancers	NHEK	skin
28	chr9:22030200-22030600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr9:22030200-22030600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:22030200-22030600	Enhancers	Fetal Intestine Large	intestine
31	chr9:22030200-22030800	Enhancers	Stomach Mucosa	stomach
32	chr9:22030200-22030800	Enhancers	HSMMtube	muscle
33	chr9:22030200-22037400	Weak transcription	Primary B cells from cord blood	blood
34	chr9:22030400-22030800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr9:22030400-22031000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:22030400-22031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:22030400-22032000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:22030400-22035400	Weak transcription	HSMM	muscle
39	chr9:22030400-22038000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr9:22030400-22040000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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