Variant report

Variant	rs4522209
Chromosome Location	chr12:122325971-122325972
allele	A/C
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	RAD21	chr12:122325879-122327331	HCT-116	colon:	n/a	chr12:122327047-122327056
2	IRF1	chr12:122325781-122327382	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326622-122326636 chr12:122326677-122326691
3	MAX	chr12:122325932-122327531	A549	lung:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
4	TEAD4	chr12:122325890-122327491	K562	blood:	n/a	n/a
5	SP1	chr12:122325923-122327277	HCT-116	colon:	n/a	chr12:122326625-122326634 chr12:122326625-122326635 chr12:122326677-122326689 chr12:122326625-122326635 chr12:122326624-122326636 chr12:122326625-122326639 chr12:122326624-122326636 chr12:122326625-122326634 chr12:122326626-122326635
6	TCF12	chr12:122325942-122327687	A549	lung:	n/a	n/a
7	CBX3	chr12:122325917-122326923	K562	blood:	n/a	n/a
8	GABPA	chr12:122325657-122327323	MCF-7	breast:	n/a	n/a
9	RAD21	chr12:122325658-122327980	SK-N-SH	brain:	n/a	chr12:122327716-122327735 chr12:122327047-122327056
10	CTCF	chr12:122325636-122327917	SK-N-SH	brain:	n/a	chr12:122326573-122326586 chr12:122327723-122327731 chr12:122327719-122327735 chr12:122327713-122327734
11	CBX3	chr12:122325901-122327226	HCT-116	colon:	n/a	n/a
12	JUN	chr12:122325490-122327909	K562	blood:	n/a	chr12:122326468-122326476 chr12:122326467-122326477 chr12:122326466-122326478 chr12:122326467-122326477
13	SIN3AK20	chr12:122325968-122327475	MCF-7	breast:	n/a	n/a
14	NR2F2	chr12:122325929-122326843	K562	blood:	n/a	n/a
15	HCFC1	chr12:122325619-122327601	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:122325941-122327040	PANC-1	pancreas:	n/a	n/a
17	CTCF	chr12:122325802-122327877	A549	lung:	n/a	chr12:122326573-122326586 chr12:122327723-122327731 chr12:122327719-122327735 chr12:122327713-122327734
18	RAD21	chr12:122325748-122327278	HCT-116	colon:	n/a	chr12:122327047-122327056
19	GABPA	chr12:122325866-122327112	A549	lung:	n/a	n/a
20	GATA3	chr12:122325913-122326890	MCF-7	breast:	n/a	chr12:122326471-122326478
21	MAX	chr12:122325713-122327420	HCT-116	colon:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
22	MYC	chr12:122325917-122326963	MCF10A-Er-Src	breast:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
23	CBX3	chr12:122325929-122327525	K562	blood:	n/a	n/a
24	TEAD4	chr12:122325898-122327389	K562	blood:	n/a	n/a
25	MXI1	chr12:122325562-122328031	SK-N-SH	brain:	n/a	n/a
26	REST	chr12:122325900-122327337	H1-neurons	neurons:	n/a	n/a
27	RCOR1	chr12:122325861-122327182	HepG2	liver:	n/a	n/a
28	MAX	chr12:122325886-122327324	HCT-116	colon:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
29	SP1	chr12:122325959-122327293	A549	lung:	n/a	chr12:122326625-122326634 chr12:122326625-122326635 chr12:122326677-122326689 chr12:122326625-122326635 chr12:122326624-122326636 chr12:122326625-122326639 chr12:122326624-122326636 chr12:122326625-122326634 chr12:122326626-122326635
30	KAP1	chr12:122325936-122327604	HEK293	kidney:	n/a	n/a
31	GATA3	chr12:122325836-122327353	A549	lung:	n/a	chr12:122326471-122326478 chr12:122327281-122327288
32	BCL3	chr12:122325970-122327471	A549	lung:	n/a	chr12:122326467-122326476 chr12:122326721-122326734
33	MYC	chr12:122325513-122327168	A549	lung:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
34	PML	chr12:122325785-122327626	GM12878	blood:	n/a	n/a
35	USF1	chr12:122325871-122327255	HCT-116	colon:	n/a	n/a
36	GATA1	chr12:122325874-122327560	PBDE	blood:	n/a	chr12:122326471-122326478 chr12:122327281-122327288
37	SETDB1	chr12:122325962-122326718	U2OS	brain:	n/a	n/a
38	STAT5A	chr12:122325928-122327228	K562	blood:	n/a	n/a
39	POLR2A	chr12:122325956-122327170	SK-N-MC	brain:	n/a	n/a
40	GATA3	chr12:122325967-122326815	T-47D	breast:	n/a	chr12:122326471-122326478
41	SP1	chr12:122325882-122327238	A549	lung:	n/a	chr12:122326625-122326634 chr12:122326625-122326635 chr12:122326677-122326689 chr12:122326625-122326635 chr12:122326624-122326636 chr12:122326625-122326639 chr12:122326624-122326636 chr12:122326625-122326634 chr12:122326626-122326635
42	FOSL2	chr12:122325818-122327282	A549	lung:	n/a	chr12:122326468-122326476 chr12:122326467-122326477 chr12:122326466-122326478 chr12:122326465-122326476 chr12:122326467-122326477
43	GATA2	chr12:122325958-122326629	HUVEC	blood vessel:	n/a	chr12:122326471-122326478
44	ARID3A	chr12:122325816-122326760	HepG2	liver:	n/a	n/a
45	MTA3	chr12:122325960-122327195	GM12878	blood:	n/a	n/a
46	REST	chr12:122325898-122327214	A549	lung:	n/a	n/a
47	TRIM28	chr12:122325931-122327435	K562	blood:	n/a	n/a
48	MTA3	chr12:122325882-122327336	GM12878	blood:	n/a	n/a
49	NR2F2	chr12:122325857-122327759	K562	blood:	n/a	n/a
50	GATA3	chr12:122325682-122326376	SH-SY5Y	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:122325929-122325979	GM12891	blood:	n/a
2	chr12:122325929-122325979	IMR90	lung:	fetal
3	chr12:122325929-122325979	AG09309	skin:	n/a
4	chr12:122325929-122325979	GM12878	blood:	n/a
5	chr12:122325929-122325979	SAEC	small airway:	n/a
6	chr12:122325929-122325979	NHDF-neo	bronchial:	n/a
7	chr12:122325929-122325979	PFSK-1	brain:	n/a
8	chr12:122325929-122325979	HepG2	liver:	n/a
9	chr12:122325929-122325979	GM19239	blood:	n/a
10	chr12:122325929-122325979	HCT-116	colon:	n/a
11	chr12:122325929-122325979	CMK	blood:	n/a
12	chr12:122325929-122325979	Hepatocyte	liver:	n/a
13	chr12:122325929-122325979	BE2_C	brain:	n/a
14	chr12:122325929-122325979	H1-hESC	embryonic stem cell:	embryo
15	chr12:122325929-122325979	AG04450	lung:	fetal
16	chr12:122325929-122325979	PrEC	prostate:	n/a
17	chr12:122325929-122325979	SK-N-SH_RA	brain:	n/a
18	chr12:122325929-122325979	HEEpiC	esophagus:	n/a
19	chr12:122325929-122325979	HRCEpiC	kidney:	n/a
20	chr12:122325929-122325979	HCPEpiC	choroid plexus:	n/a
21	chr12:122325929-122325979	MCF-7	breast:	n/a
22	chr12:122325929-122325979	ovcar-3	ovarian:	n/a
23	chr12:122325929-122325979	K562	blood:	n/a
24	chr12:122325929-122325979	HIPEpiC	eye:	n/a
25	chr12:122325929-122325979	Jurkat	blood:	n/a
26	chr12:122325929-122325979	U87	brain:	n/a
27	chr12:122325929-122325979	HCM	heart:	n/a
28	chr12:122325929-122325979	HPAEpiC	pulmonary alveolar:	n/a
29	chr12:122325929-122325979	MCF10A-Er-Src	breast:	n/a
30	chr12:122325929-122325979	AG10803	skin:	n/a
31	chr12:122325929-122325979	GM12892	blood:	n/a
32	chr12:122325929-122325979	HEK293	kidney:	embryo
33	chr12:122325929-122325979	ECC-1	luminal epithelium:	n/a
34	chr12:122325929-122325979	HUVEC	blood vessel:	n/a
35	chr12:122325929-122325979	ProgFib	skin:	n/a
36	chr12:122325929-122325979	AG09319	gingival:	n/a
37	chr12:122325929-122325979	NT2-D1	testis:	n/a
38	chr12:122325929-122325979	NB4	blood:	n/a
39	chr12:122325929-122325979	HRPEpiC	eye:	n/a
40	chr12:122325929-122325979	Hela-S3	cervix:	n/a
41	chr12:122325929-122325979	HCF	heart:	n/a
42	chr12:122325929-122325979	BJ	skin:	n/a
43	chr12:122325929-122325979	SK-N-MC	brain:	n/a
44	chr12:122325929-122325979	HNPCEpiC	eye:	n/a
45	chr12:122325929-122325979	Caco-2	colon:	n/a
46	chr12:122325929-122325979	SK-N-SH	brain:	n/a
47	chr12:122325929-122325979	LNCaP	prostate:	n/a
48	chr12:122325929-122325979	AoSMC	blood vessel:	n/a
49	chr12:122325929-122325979	RPTEC	kidney:	n/a
50	chr12:122325929-122325979	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122325656..122327392-chr12:122459155..122461282,2	K562	blood:
2	chr12:122234754..122235555-chr12:122325940..122326563,2	MCF-7	breast:
3	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
4	chr12:122321753..122324282-chr12:122324684..122326491,2	K562	blood:
5	chr12:122213395..122216201-chr12:122325531..122328146,2	MCF-7	breast:
6	chr12:122232032..122233517-chr12:122325701..122326925,10	MCF-7	breast:
7	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
8	chr12:122214229..122218603-chr12:122325636..122328202,4	MCF-7	breast:
9	chr12:122319572..122322353-chr12:122324355..122326595,2	MCF-7	breast:
10	chr12:122325518..122327854-chr12:122516363..122518486,3	K562	blood:
11	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
12	chr12:122325172..122329151-chr12:122329541..122333817,7	MCF-7	breast:
13	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
14	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256950	TF binding region
PSMD9	TF binding region
PSMD9	CpG island
ENSG00000256950	CpG island
ENSG00000139725	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1824949	0.80[EUR][1000 genomes]
rs2004863	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2004864	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2076860	1.00[ASW][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs2272132	1.00[ASW][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2596142	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3741581	0.80[EUR][1000 genomes]
rs55778445	0.80[EUR][1000 genomes]
rs58026220	0.80[EUR][1000 genomes]
rs58158474	0.80[EUR][1000 genomes]
rs58642707	0.93[EUR][1000 genomes]
rs59695002	0.93[EUR][1000 genomes]
rs60620185	0.80[EUR][1000 genomes]
rs61661595	1.00[ASN][1000 genomes]
rs6486793	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7138299	0.80[EUR][1000 genomes]
rs7138556	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7294535	0.80[EUR][1000 genomes]
rs7303779	0.87[EUR][1000 genomes]
rs7314352	0.80[EUR][1000 genomes]
rs830125	0.80[EUR][1000 genomes]
rs872781	0.80[EUR][1000 genomes]
rs884785	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs884786	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4522209	RBM46	trans	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122321400-122326000	Weak transcription	Right Atrium	heart
2	chr12:122321400-122326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:122321400-122326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122321800-122326000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:122322000-122326000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:122323400-122326000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:122325600-122326000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:122325600-122326000	Enhancers	Liver	Liver
9	chr12:122325600-122326200	Flanking Active TSS	A549	lung
10	chr12:122325600-122326400	Flanking Active TSS	Dnd41	blood
11	chr12:122325800-122326000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:122325800-122326000	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:122325800-122326000	Enhancers	Primary T cells from cord blood	blood
14	chr12:122325800-122326000	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr12:122325800-122326000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:122325800-122326000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:122325800-122326000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:122325800-122326000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:122325800-122326000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr12:122325800-122326000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:122325800-122326000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:122325800-122326000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:122325800-122326000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:122325800-122326000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:122325800-122326000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:122325800-122326000	Enhancers	Adipose Nuclei	Adipose
27	chr12:122325800-122326000	Enhancers	Brain Angular Gyrus	brain
28	chr12:122325800-122326000	Enhancers	Brain Anterior Caudate	brain
29	chr12:122325800-122326000	Active TSS	Brain Cingulate Gyrus	brain
30	chr12:122325800-122326000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:122325800-122326000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:122325800-122326000	Enhancers	Colon Smooth Muscle	Colon
33	chr12:122325800-122326000	Enhancers	Duodenum Mucosa	Duodenum
34	chr12:122325800-122326000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:122325800-122326000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:122325800-122326000	Enhancers	Fetal Kidney	kidney
37	chr12:122325800-122326000	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:122325800-122326000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:122325800-122326000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:122325800-122326000	Enhancers	HMEC	breast
41	chr12:122325800-122326000	Enhancers	HSMMtube	muscle
42	chr12:122325800-122326000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr12:122325800-122326000	Enhancers	NHDF-Ad	bronchial
44	chr12:122325800-122326200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:122325800-122326200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr12:122325800-122326400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:122325800-122326400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:122325800-122326400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr12:122325800-122326400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr12:122325800-122326400	Flanking Active TSS	GM12878-XiMat	blood

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