Variant report

Variant	rs2282044
Chromosome Location	chr9:22446672-22446673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:22446620-22447666	MCF-7	breast:	n/a	n/a
2	NFYB	chr9:22446359-22446814	Hela-S3	cervix:	n/a	chr9:22446672-22446687
3	MAX	chr9:22446278-22448068	A549	lung:	n/a	n/a
4	MAX	chr9:22446469-22447698	Hela-S3	cervix:	n/a	n/a
5	E2F6	chr9:22446333-22446842	H1-hESC	embryonic stem cell:	n/a	chr9:22446688-22446697
6	BACH1	chr9:22446601-22447549	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:22446558-22447694	MCF-7	breast:	n/a	n/a
8	TCF7L2	chr9:22446630-22447773	Hela-S3	cervix:	n/a	n/a
9	E2F4	chr9:22446606-22446916	MCF10A-Er-Src	breast:	n/a	chr9:22446688-22446697
10	CTCF	chr9:22446613-22448844	A549	lung:	n/a	n/a
11	RAD21	chr9:22446638-22447690	H1-hESC	embryonic stem cell:	n/a	chr9:22446691-22446703
12	ELF1	chr9:22446400-22447162	MCF-7	breast:	n/a	chr9:22446750-22446762
13	MAX	chr9:22446318-22447023	ECC-1	luminal epithelium:	n/a	n/a
14	NFYA	chr9:22446504-22446799	Hela-S3	cervix:	n/a	n/a
15	TBP	chr9:22446667-22447648	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr9:22446660-22446810	SAEC	small airway:	n/a	n/a
17	POLR2A	chr9:22446590-22447785	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:22446583-22447633	HUVEC	blood vessel:	n/a	n/a
19	MAX	chr9:22446430-22446860	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr9:22446577-22448100	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr9:22446412-22447134	A549	lung:	n/a	n/a
22	GTF2F1	chr9:22446510-22446710	H1-hESC	embryonic stem cell:	n/a	n/a
23	ELF1	chr9:22446587-22447284	MCF-7	breast:	n/a	chr9:22446750-22446762
24	CREB1	chr9:22446558-22446822	A549	lung:	n/a	n/a
25	TAF1	chr9:22446618-22447982	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr9:22446658-22447010	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr9:22446669-22447561	Hela-S3	cervix:	n/a	n/a
28	E2F6	chr9:22446232-22446981	A549	lung:	n/a	chr9:22446688-22446697
29	MAZ	chr9:22446536-22447952	Hela-S3	cervix:	n/a	n/a
30	HDAC2	chr9:22446552-22447458	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD2	chr9:22446579-22447049	Hela-S3	cervix:	n/a	chr9:22446718-22446728
32	RFX5	chr9:22446445-22447609	Hela-S3	cervix:	n/a	n/a
33	CTBP2	chr9:22446617-22448118	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr9:22446655-22447123	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF263	chr9:22446638-22448412	HEK293-T-REx	kidney:	n/a	chr9:22446654-22446663 chr9:22446697-22446706
36	E2F6	chr9:22446488-22446863	A549	lung:	n/a	chr9:22446688-22446697
37	SP1	chr9:22446429-22447089	A549	lung:	n/a	chr9:22446769-22446778 chr9:22446719-22446728 chr9:22446720-22446729 chr9:22446990-22447004 chr9:22446767-22446779 chr9:22446768-22446777 chr9:22446769-22446778 chr9:22446767-22446779 chr9:22446768-22446778 chr9:22446718-22446730 chr9:22446719-22446728 chr9:22446768-22446778
38	MAX	chr9:22446458-22446690	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr9:22446556-22447133	MCF-7	breast:	n/a	n/a
40	RCOR1	chr9:22446562-22448243	Hela-S3	cervix:	n/a	n/a
41	E2F6	chr9:22446450-22446904	H1-hESC	embryonic stem cell:	n/a	chr9:22446688-22446697
42	POLR2A	chr9:22446619-22447691	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:22402119..22404171-chr9:22444827..22446805,2	MCF-7	breast:

Variant related genes	Relation type
DMRTA1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12551118	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12551804	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12552243	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12552720	0.87[ASN][1000 genomes]
rs12554657	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1571487	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16906134	0.95[ASN][1000 genomes]
rs16906176	1.00[AMR][1000 genomes]
rs16906196	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1031822	chr9:22364573-22490686	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv892750	chr9:22383816-22496640	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1016983	chr9:22412948-22672062	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1027227	chr9:22416348-22666768	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv540088	chr9:22416348-22666768	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22446000-22450400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:22446200-22446800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:22446200-22447000	Active TSS	Stomach Smooth Muscle	stomach
4	chr9:22446200-22447600	Active TSS	NH-A	brain
5	chr9:22446200-22447800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:22446200-22447800	Active TSS	Aorta	Aorta
7	chr9:22446200-22447800	Active TSS	Colon Smooth Muscle	Colon
8	chr9:22446200-22449000	Active TSS	Brain Anterior Caudate	brain
9	chr9:22446200-22449200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr9:22446200-22449600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:22446200-22450000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:22446400-22446800	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr9:22446400-22446800	Bivalent/Poised TSS	Fetal Lung	lung
14	chr9:22446400-22446800	Active TSS	Fetal Muscle Leg	muscle
15	chr9:22446400-22446800	Active TSS	Fetal Stomach	stomach
16	chr9:22446400-22447000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:22446400-22447000	Active TSS	Left Ventricle	heart
18	chr9:22446400-22447200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:22446400-22447200	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr9:22446400-22447200	Active TSS	Colonic Mucosa	Colon
21	chr9:22446400-22447400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr9:22446400-22447600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:22446400-22447600	Active TSS	HSMMtube	muscle
24	chr9:22446400-22447600	Active TSS	NHLF	lung
25	chr9:22446400-22447800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:22446400-22448000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr9:22446400-22448000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:22446400-22448000	Active TSS	Brain Angular Gyrus	brain
29	chr9:22446400-22448000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr9:22446400-22448000	Active TSS	Brain Substantia Nigra	brain
31	chr9:22446400-22448000	Active TSS	Psoas Muscle	Psoas
32	chr9:22446400-22448000	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr9:22446400-22448000	Active TSS	HMEC	breast
34	chr9:22446400-22448200	Active TSS	Pancreas	Pancrea
35	chr9:22446400-22448200	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr9:22446400-22448200	Active TSS	Right Atrium	heart
37	chr9:22446400-22448200	Active TSS	NHEK	skin
38	chr9:22446400-22448400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:22446400-22448400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:22446400-22448400	Active TSS	Gastric	stomach
41	chr9:22446400-22449000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:22446400-22449000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:22446400-22449200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr9:22446400-22449200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:22446400-22449200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:22446400-22449400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr9:22446600-22446800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:22446600-22446800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr9:22446600-22446800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr9:22446600-22446800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--

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