Variant report

Variant	rs2069422
Chromosome Location	chr9:22008026-22008027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:22007980-22008130	HPAF	blood vessel:	n/a	n/a
2	CHD1	chr9:22007880-22009989	IMR90	lung:	n/a	n/a
3	POLR2A	chr9:22007801-22009751	H1-neurons	neurons:	n/a	n/a
4	CTCF	chr9:22007920-22008070	HPAF	blood vessel:	n/a	n/a
5	POLR2A	chr9:22007993-22009814	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:22007891-22009895	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr9:22007656-22009795	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:22005608..22009530-chr9:22211237..22215024,4	MCF-7	breast:
2	chr9:21992827..21995558-chr9:22007456..22010608,5	MCF-7	breast:
3	chr9:21800247..21802715-chr9:22007122..22010872,3	MCF-7	breast:
4	chr9:22007147..22011040-chr9:22011810..22014340,4	MCF-7	breast:
5	chr9:22007424..22010079-chr9:22214224..22216298,2	MCF-7	breast:

No data

Variant related genes	Relation type
UBA52P6	TF binding region
CDKN2B	TF binding region
ENSG00000264545	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000215221	Chromatin interaction
ENSG00000236921	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000147889	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

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[ASW][hapmap];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];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1333035	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17694493	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17694572	0.82[AMR][1000 genomes]
rs17756311	0.82[AMR][1000 genomes]
rs2069426	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[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];0.98[EUR][1000 genomes]
rs3218002	0.86[EUR][1000 genomes]
rs3218005	0.86[EUR][1000 genomes]
rs3218007	0.86[EUR][1000 genomes]
rs3218018	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[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[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662463	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]
rs974336	1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][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	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
4	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
5	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
6	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
7	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
8	nsv892748	chr9:22005647-22011642	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv613760	chr9:22006269-22009960	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv973479	chr9:22006327-22010710	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2069422	CDKN2B	cis	Whole Blood	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21995800-22008400	Weak transcription	Aorta	Aorta
2	chr9:22005000-22008400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr9:22005600-22009400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:22005800-22009800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:22006200-22008600	Weak transcription	Gastric	stomach
6	chr9:22006200-22008600	Weak transcription	Lung	lung
7	chr9:22006200-22008800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:22006200-22009600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:22006400-22008200	Active TSS	Adipose Nuclei	Adipose
10	chr9:22006400-22008400	Weak transcription	Right Ventricle	heart
11	chr9:22006400-22008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:22006400-22008600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:22006400-22008600	Weak transcription	Pancreas	Pancrea
14	chr9:22006400-22009400	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr9:22006400-22009400	Active TSS	HMEC	breast
16	chr9:22006400-22010000	Active TSS	Muscle Satellite Cultured Cells	--
17	chr9:22006400-22010000	Active TSS	HSMMtube	muscle
18	chr9:22006600-22009400	Active TSS	Duodenum Mucosa	Duodenum
19	chr9:22006600-22009400	Active TSS	Hela-S3	cervix
20	chr9:22006600-22009400	Active TSS	NHEK	skin
21	chr9:22006600-22009600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:22006600-22009600	Active TSS	NHLF	lung
23	chr9:22006600-22010000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:22006800-22010000	Active TSS	NH-A	brain
25	chr9:22007200-22009400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr9:22007400-22008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:22007400-22008600	Weak transcription	Esophagus	oesophagus
28	chr9:22007400-22008600	Genic enhancers	Dnd41	blood
29	chr9:22007400-22009600	Active TSS	NHDF-Ad	bronchial
30	chr9:22007400-22010000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr9:22007600-22009600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:22007800-22008200	Bivalent Enhancer	HUVEC	blood vessel
33	chr9:22007800-22008400	Bivalent Enhancer	Primary B cells from cord blood	blood
34	chr9:22007800-22009800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr9:22007800-22009800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr9:22008000-22008200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:22008000-22008200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:22008000-22008200	Enhancers	Brain Anterior Caudate	brain
39	chr9:22008000-22008200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr9:22008000-22008200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr9:22008000-22008400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:22008000-22008400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:22008000-22008400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:22008000-22008400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
45	chr9:22008000-22008400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:22008000-22008400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr9:22008000-22008400	Flanking Active TSS	Osteobl	bone
48	chr9:22008000-22008600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:22008000-22008600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
50	chr9:22008000-22008600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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