Variant report

Variant	rs17756311
Chromosome Location	chr9:22053895-22053896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:22051930..22054348-chr9:22086021..22088331,2	MCF-7	breast:
2	chr9:22051697..22054295-chr9:22107294..22109558,2	MCF-7	breast:
3	chr9:22051314..22055495-chr9:22237121..22240202,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTAP-1	chr9:22051172-22054011	NONHSAT130430

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1333034	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1333035	0.80[EUR][1000 genomes]
rs17694493	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17694555	0.95[EUR][1000 genomes]
rs17694572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069422	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs2069426	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2811709	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2811712	1.00[MEX][hapmap]
rs3218002	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3218005	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3218007	0.85[EUR][1000 genomes]
rs3218018	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3731246	1.00[CEU][hapmap]
rs598664	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs662463	1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs974336	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17756311	CDKN2B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22049400-22054000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr9:22051200-22055600	Weak transcription	Esophagus	oesophagus
3	chr9:22051800-22054000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:22051800-22054000	Enhancers	HMEC	breast
5	chr9:22051800-22056000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:22052000-22054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:22052000-22058200	Weak transcription	Primary B cells from cord blood	blood
8	chr9:22052000-22059200	Strong transcription	Dnd41	blood
9	chr9:22052400-22054200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:22052400-22054400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:22053000-22055400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:22053200-22055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:22053200-22061200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:22053400-22054000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr9:22053600-22054600	Enhancers	NH-A	brain
16	chr9:22053600-22055200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:22053600-22055200	Weak transcription	HSMMtube	muscle
18	chr9:22053600-22057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:22053800-22057200	Weak transcription	HUVEC	blood vessel
20	chr9:22053800-22058600	Weak transcription	Osteobl	bone
21	chr9:22053800-22059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:22053800-22059800	Weak transcription	HSMM	muscle
23	chr9:22053800-22060000	Weak transcription	NHLF	lung
24	chr9:22053800-22061200	Weak transcription	NHDF-Ad	bronchial
25	chr9:22053800-22061400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:22053800-22065200	Weak transcription	NHEK	skin
27	chr9:22053800-22069000	Weak transcription	Hela-S3	cervix
28	chr9:22053800-22079800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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