Variant report

Variant	rs34014405
Chromosome Location	chr12:49211913-49211914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49211741-49213179	HUVEC	blood vessel:	n/a	n/a
2	HMGN3	chr12:49211816-49212388	K562	blood:	n/a	n/a
3	TCF12	chr12:49211795-49212618	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr12:49211697-49213242	A549	lung:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
5	MAX	chr12:49211624-49213172	MCF-7	breast:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
6	MAZ	chr12:49211338-49213204	IMR90	lung:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
7	POLR2A	chr12:49211885-49212195	Raji	blood:	n/a	n/a
8	ZBTB7A	chr12:49211551-49212963	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr12:49211722-49212420	A549	lung:	n/a	n/a
10	FOXA1	chr12:49211727-49212008	T-47D	breast:	n/a	n/a
11	MAX	chr12:49211597-49212848	ECC-1	luminal epithelium:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
12	POLR2A	chr12:49211754-49211998	ProgFib	skin:	n/a	n/a
13	POLR2A	chr12:49211898-49212817	HUVEC	blood vessel:	n/a	n/a
14	ZNF263	chr12:49211641-49212468	HEK293-T-REx	kidney:	n/a	chr12:49212282-49212291 chr12:49212273-49212282 chr12:49212238-49212247
15	CEBPB	chr12:49211633-49211927	H1-hESC	embryonic stem cell:	n/a	chr12:49211794-49211805
16	POLR2A	chr12:49211731-49212949	H1-neurons	neurons:	n/a	n/a
17	ELF1	chr12:49211647-49212464	MCF-7	breast:	n/a	chr12:49212290-49212302
18	POLR2A	chr12:49211875-49212427	K562	blood:	n/a	n/a
19	CEBPB	chr12:49211565-49212005	MCF-7	breast:	n/a	chr12:49211794-49211805
20	POLR2A	chr12:49211573-49212659	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:49211704-49212767	PFSK-1	brain:	n/a	n/a
22	MAX	chr12:49211913-49212431	K562	blood:	n/a	chr12:49212289-49212299
23	POLR2A	chr12:49211589-49212629	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr12:49211653-49212496	MCF-7	breast:	n/a	n/a
25	SIN3AK20	chr12:49211846-49212525	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr12:49211877-49212477	HCT-116	colon:	n/a	n/a
27	SIN3A	chr12:49211438-49213350	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:49211802-49211990	Gliobla	brain:	n/a	n/a
29	CTBP2	chr12:49211806-49213590	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:49211297-49212598	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr12:49211719-49212569	PFSK-1	brain:	n/a	n/a
32	CEBPB	chr12:49211661-49211949	IMR90	lung:	n/a	chr12:49211794-49211805
33	ELF1	chr12:49211602-49212946	GM12878	blood:	n/a	chr12:49212290-49212302
34	ZBTB7A	chr12:49211849-49212212	K562	blood:	n/a	n/a
35	POLR2A	chr12:49211881-49212461	PANC-1	pancreas:	n/a	n/a
36	REST	chr12:49211494-49213099	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr12:49211768-49212499	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr12:49211846-49212449	A549	lung:	n/a	n/a
39	TAF1	chr12:49211905-49212514	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr12:49211659-49212824	MCF-7	breast:	n/a	n/a
41	TAF1	chr12:49211856-49212498	H1-neurons	neurons:	n/a	n/a
42	JUND	chr12:49211814-49212355	A549	lung:	n/a	chr12:49211912-49211926
43	POLR2A	chr12:49211904-49212404	HUVEC	blood vessel:	n/a	n/a
44	HDAC2	chr12:49211816-49213166	MCF-7	breast:	n/a	chr12:49212832-49212851
45	POLR2A	chr12:49211745-49212456	ECC-1	luminal epithelium:	n/a	n/a
46	EGR1	chr12:49211881-49213047	HCT-116	colon:	n/a	chr12:49212966-49212979 chr12:49212514-49212524 chr12:49212428-49212438 chr12:49212232-49212242 chr12:49212499-49212514 chr12:49212777-49212787 chr12:49212393-49212407 chr12:49212774-49212787
47	POLR2A	chr12:49211786-49213003	H1-neurons	neurons:	n/a	n/a
48	ZBTB7A	chr12:49211432-49213215	ECC-1	luminal epithelium:	n/a	n/a
49	ZNF263	chr12:49211730-49212289	K562	blood:	n/a	chr12:49212273-49212282 chr12:49212238-49212247
50	PML	chr12:49211872-49212403	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49211867-49211917	AG10803	skin:	n/a
2	chr12:49211867-49211917	HCM	heart:	n/a
3	chr12:49211867-49211917	AG04450	lung:	fetal
4	chr12:49211867-49211917	HL-60	blood:	n/a
5	chr12:49211867-49211917	HCPEpiC	choroid plexus:	n/a
6	chr12:49211867-49211917	PANC-1	pancreas:	n/a
7	chr12:49211867-49211917	NT2-D1	testis:	n/a
8	chr12:49211867-49211917	NH-A	brain:	n/a
9	chr12:49211867-49211917	MCF-7	breast:	n/a
10	chr12:49211867-49211917	GM06990	blood:	n/a
11	chr12:49211867-49211917	HCF	heart:	n/a
12	chr12:49211867-49211917	HPAEpiC	pulmonary alveolar:	n/a
13	chr12:49211867-49211917	ProgFib	skin:	n/a
14	chr12:49211867-49211917	HCT-116	colon:	n/a
15	chr12:49211867-49211917	PFSK-1	brain:	n/a
16	chr12:49211867-49211917	GM12891	blood:	n/a
17	chr12:49211867-49211917	HUVEC	blood vessel:	n/a
18	chr12:49211867-49211917	MCF10A-Er-Src	breast:	n/a
19	chr12:49211867-49211917	HNPCEpiC	eye:	n/a
20	chr12:49211867-49211917	HRE	kidney:	n/a
21	chr12:49211867-49211917	HMEC	breast:	n/a
22	chr12:49211867-49211917	NHDF-neo	bronchial:	n/a
23	chr12:49211867-49211917	ECC-1	luminal epithelium:	n/a
24	chr12:49211867-49211917	HRCEpiC	kidney:	n/a
25	chr12:49211867-49211917	Hepatocyte	liver:	n/a
26	chr12:49211867-49211917	RPTEC	kidney:	n/a
27	chr12:49211867-49211917	AG04449	skin:	fetal
28	chr12:49211867-49211917	BE2_C	brain:	n/a
29	chr12:49211867-49211917	AG09309	skin:	n/a
30	chr12:49211867-49211917	CMK	blood:	n/a
31	chr12:49211867-49211917	Caco-2	colon:	n/a
32	chr12:49211867-49211917	T-47D	breast:	n/a
33	chr12:49211867-49211917	SAEC	small airway:	n/a
34	chr12:49211867-49211917	GM12892	blood:	n/a
35	chr12:49211867-49211917	Jurkat	blood:	n/a
36	chr12:49211867-49211917	SKMC	muscle:	n/a
37	chr12:49211867-49211917	GM19239	blood:	n/a
38	chr12:49211867-49211917	BJ	skin:	n/a
39	chr12:49211867-49211917	IMR90	lung:	fetal
40	chr12:49211867-49211917	K562	blood:	n/a
41	chr12:49211867-49211917	AoSMC	blood vessel:	n/a
42	chr12:49211867-49211917	HepG2	liver:	n/a
43	chr12:49211867-49211917	PrEC	prostate:	n/a
44	chr12:49211867-49211917	SK-N-SH_RA	brain:	n/a
45	chr12:49211867-49211917	SK-N-MC	brain:	n/a
46	chr12:49211867-49211917	AG09319	gingival:	n/a
47	chr12:49211867-49211917	Hela-S3	cervix:	n/a
48	chr12:49211867-49211917	H1-hESC	embryonic stem cell:	embryo
49	chr12:49211867-49211917	HEK293	kidney:	embryo
50	chr12:49211867-49211917	LNCaP	prostate:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49207378..49214966-chr12:49243991..49247655,21	MCF-7	breast:
2	chr12:49203980..49213270-chr12:49239370..49250118,15	MCF-7	breast:
3	chr12:49211386..49213758-chr12:49317822..49319346,2	MCF-7	breast:
4	chr12:48917515..48920061-chr12:49210634..49213027,2	MCF-7	breast:
5	chr12:49210034..49212452-chr12:49258517..49260819,2	MCF-7	breast:
6	chr12:49180478..49186692-chr12:49206898..49214052,14	MCF-7	breast:
7	chr12:49210248..49212975-chr12:49452451..49454269,2	MCF-7	breast:
8	chr12:49211113..49212754-chr12:49254899..49256730,2	MCF-7	breast:
9	chr12:49210476..49213723-chr12:49348025..49351364,4	MCF-7	breast:
10	chr12:49211388..49215233-chr12:49215394..49218773,9	MCF-7	breast:
11	chr12:49211292..49213988-chr21:44527070..44529519,2	MCF-7	breast:
12	chr12:49073658..49078597-chr12:49201352..49212442,12	MCF-7	breast:
13	chr12:49211648..49214414-chr12:49216563..49220166,3	K562	blood:
14	chr12:49209305..49214344-chr12:49410836..49414443,6	MCF-7	breast:
15	chr12:49211671..49216078-chr12:49223480..49227983,7	MCF-7	breast:
16	chr12:49211528..49213984-chr12:49245002..49247002,2	K562	blood:

No data

Variant related genes	Relation type
CACNB3	TF binding region
CACNB3	CpG island
ENSG00000181929	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000197376	Chromatin interaction
ENSG00000257660	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11168749	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168751	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369114	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369130	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814893	1.00[ASN][1000 genomes]
rs2453467	1.00[ASN][1000 genomes]
rs36000595	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730308	1.00[ASN][1000 genomes]
rs55638074	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916159	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34014405	CACNB3	Cis_1M	lymphoblastoid	RTeQTL
rs34014405	CACNB3	cis	cerebellum	SCAN
rs34014405	ARID2	cis	parietal	SCAN
rs34014405	CACNB3	cis	parietal	SCAN
rs34014405	AQP2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49209400-49212000	Flanking Active TSS	Dnd41	blood
2	chr12:49209800-49212200	Weak transcription	Small Intestine	intestine
3	chr12:49209800-49213600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:49211000-49212000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49211000-49212200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:49211200-49212000	Flanking Active TSS	Fetal Brain Male	brain
7	chr12:49211200-49212000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:49211200-49212000	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr12:49211400-49212000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:49211400-49212000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:49211400-49212000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:49211400-49212000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:49211400-49212000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr12:49211400-49212000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:49211400-49212000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr12:49211400-49212000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr12:49211400-49212000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:49211400-49212000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:49211400-49212000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr12:49211400-49212000	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr12:49211400-49212000	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr12:49211400-49212000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:49211400-49212000	Flanking Active TSS	NH-A	brain
24	chr12:49211400-49212000	Flanking Active TSS	NHLF	lung
25	chr12:49211400-49212200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr12:49211400-49212200	Flanking Active TSS	Colonic Mucosa	Colon
27	chr12:49211400-49212200	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr12:49211400-49212200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr12:49211400-49213800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:49211600-49212000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr12:49211600-49212000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:49211600-49212000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr12:49211600-49212000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:49211600-49212000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:49211600-49212000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
36	chr12:49211600-49212000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr12:49211600-49212000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
38	chr12:49211600-49212000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:49211600-49212000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:49211600-49212000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:49211600-49212000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr12:49211600-49212000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:49211600-49212000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:49211600-49212000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:49211600-49212000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:49211600-49212000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
47	chr12:49211600-49212000	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr12:49211600-49212000	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr12:49211600-49212000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr12:49211600-49212000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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