Variant report

Variant	rs12369114
Chromosome Location	chr12:49212806-49212807
allele	C/T
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	CTCF	chr12:49212780-49212930	NHDF-neo	bronchial:	n/a	n/a
2	POLR2A	chr12:49211741-49213179	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr12:49212798-49212954	GM10248	blood:	n/a	n/a
4	MAZ	chr12:49211969-49212915	GM12878	blood:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
5	CTCF	chr12:49212780-49212930	MCF-7	breast:	n/a	n/a
6	CTCF	chr12:49212780-49212930	BE2_C	brain:	n/a	n/a
7	YY1	chr12:49212052-49213120	H1-hESC	embryonic stem cell:	n/a	chr12:49212779-49212788 chr12:49212591-49212605 chr12:49212288-49212297 chr12:49212517-49212528
8	RAD21	chr12:49212632-49213140	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr12:49211697-49213242	A549	lung:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
10	TCF12	chr12:49212803-49213055	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr12:49211624-49213172	MCF-7	breast:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
12	RAD21	chr12:49212734-49213014	Hela-S3	cervix:	n/a	n/a
13	CHD2	chr12:49212660-49212908	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr12:49211338-49213204	IMR90	lung:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
15	CTCF	chr12:49212776-49213036	GM12891	blood:	n/a	n/a
16	ATF2	chr12:49212572-49213014	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZBTB7A	chr12:49211551-49212963	ECC-1	luminal epithelium:	n/a	n/a
18	MAZ	chr12:49212800-49212856	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr12:49212653-49213242	MCF-7	breast:	n/a	n/a
20	CTCF	chr12:49212770-49213014	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:49212800-49212950	AG04449	skin:	n/a	n/a
22	MAX	chr12:49211597-49212848	ECC-1	luminal epithelium:	n/a	chr12:49212777-49212787 chr12:49212289-49212299 chr12:49212773-49212783
23	CHD1	chr12:49212652-49212906	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr12:49212765-49212993	GM13977	blood:	n/a	n/a
25	CTCF	chr12:49212780-49213070	GM12872	blood:	n/a	n/a
26	CTCF	chr12:49212733-49213068	MCF-7	breast:	n/a	n/a
27	CTCF	chr12:49212748-49213053	MCF-7	breast:	n/a	n/a
28	CTCF	chr12:49212773-49213038	MCF-7	breast:	n/a	n/a
29	POLR2A	chr12:49211898-49212817	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr12:49212726-49213061	MCF-7	breast:	n/a	n/a
31	CTCF	chr12:49212732-49213025	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:49211731-49212949	H1-neurons	neurons:	n/a	n/a
33	CTCF	chr12:49212546-49213173	MCF-7	breast:	n/a	chr12:49212592-49212605
34	CTCF	chr12:49212753-49213012	A549	lung:	n/a	n/a
35	CTCF	chr12:49212780-49212930	GM12872	blood:	n/a	n/a
36	EGR1	chr12:49211960-49212847	K562	blood:	n/a	chr12:49212514-49212524 chr12:49212428-49212438 chr12:49212232-49212242 chr12:49212499-49212514 chr12:49212777-49212787 chr12:49212393-49212407 chr12:49212774-49212787
37	CTCF	chr12:49212756-49213036	Medullo	brain:	n/a	n/a
38	CTCF	chr12:49212741-49212980	A549	lung:	n/a	n/a
39	CTCF	chr12:49212800-49212950	Hela-S3	cervix:	n/a	n/a
40	ATF2	chr12:49212578-49213124	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr12:49212729-49213147	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:49212791-49212817	ProgFib	skin:	n/a	n/a
43	CTCF	chr12:49212749-49213060	MCF-7	breast:	n/a	n/a
44	RAD21	chr12:49212643-49213185	MCF-7	breast:	n/a	n/a
45	CHD2	chr12:49212747-49212917	GM12878	blood:	n/a	n/a
46	CTCF	chr12:49212542-49213315	HCT-116	colon:	n/a	chr12:49212592-49212605
47	RAD21	chr12:49212793-49213014	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr12:49212780-49212930	HVMF	connective:	n/a	n/a
49	CTCF	chr12:49212718-49213130	A549	lung:	n/a	n/a
50	SIN3A	chr12:49211438-49213350	H1-hESC	embryonic stem cell:	n/a	n/a

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	chr12:49180478..49186692-chr12:49206898..49214052,14	MCF-7	breast:
6	chr12:49211960..49214574-chr12:49231587..49235207,3	MCF-7	breast:
7	chr12:49210248..49212975-chr12:49452451..49454269,2	MCF-7	breast:
8	chr12:49210476..49213723-chr12:49348025..49351364,4	MCF-7	breast:
9	chr12:49211388..49215233-chr12:49215394..49218773,9	MCF-7	breast:
10	chr12:49212473..49213308-chr12:49318055..49318794,2	MCF-7	breast:
11	chr12:49211292..49213988-chr21:44527070..44529519,2	MCF-7	breast:
12	chr12:49211648..49214414-chr12:49216563..49220166,3	K562	blood:
13	chr12:49209305..49214344-chr12:49410836..49414443,6	MCF-7	breast:
14	chr12:49211671..49216078-chr12:49223480..49227983,7	MCF-7	breast:
15	chr12:49211528..49213984-chr12:49245002..49247002,2	K562	blood:

Variant related genes	Relation type
CACNB3	TF binding region
ENSG00000257660	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000197376	Chromatin interaction
ENSG00000174233	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[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168751	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369130	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12814893	1.00[ASN][1000 genomes]
rs2453467	1.00[ASN][1000 genomes]
rs34014405	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]
rs36000595	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730308	1.00[ASN][1000 genomes]
rs55638074	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916159	0.95[AMR][1000 genomes];0.98[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
rs12369114	CACNB3	cis	parietal	SCAN
rs12369114	ARID2	cis	parietal	SCAN
rs12369114	CACNB3	cis	cerebellum	SCAN
rs12369114	CACNB3	Cis_1M	lymphoblastoid	RTeQTL
rs12369114	AQP2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49209800-49213600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:49211400-49213800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:49211600-49213000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:49211600-49213000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:49211600-49213000	Active TSS	Psoas Muscle	Psoas
6	chr12:49211600-49213000	Active TSS	HSMM	muscle
7	chr12:49211600-49213200	Active TSS	Fetal Kidney	kidney
8	chr12:49211600-49213200	Active TSS	HSMMtube	muscle
9	chr12:49211600-49213200	Active TSS	NHDF-Ad	bronchial
10	chr12:49211800-49213000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:49211800-49213000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:49211800-49213000	Active TSS	Fetal Brain Female	brain
13	chr12:49211800-49213000	Active TSS	Rectal Smooth Muscle	rectum
14	chr12:49211800-49213200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:49211800-49213200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:49211800-49213200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:49211800-49213200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:49211800-49213600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:49211800-49213600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:49212000-49213000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr12:49212000-49213000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr12:49212000-49213000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr12:49212000-49213000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:49212000-49213000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:49212000-49213000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:49212000-49213000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:49212000-49213000	Active TSS	Primary T cells from cord blood	blood
28	chr12:49212000-49213000	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:49212000-49213000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:49212000-49213000	Active TSS	Brain Substantia Nigra	brain
31	chr12:49212000-49213000	Active TSS	Colon Smooth Muscle	Colon
32	chr12:49212000-49213000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr12:49212000-49213000	Active TSS	Right Atrium	heart
34	chr12:49212000-49213000	Active TSS	NHEK	skin
35	chr12:49212000-49213200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr12:49212000-49213200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:49212000-49213200	Enhancers	Fetal Heart	heart
38	chr12:49212000-49213200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:49212000-49213200	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr12:49212000-49213200	Active TSS	NHLF	lung
41	chr12:49212000-49213200	Active TSS	Osteobl	bone
42	chr12:49212000-49213600	Active TSS	Brain Hippocampus Middle	brain
43	chr12:49212000-49214000	Active TSS	Brain Anterior Caudate	brain
44	chr12:49212000-49214200	Active TSS	Brain Cingulate Gyrus	brain
45	chr12:49212000-49214600	Active TSS	Brain Angular Gyrus	brain
46	chr12:49212000-49214600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:49212200-49213000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:49212200-49213000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:49212200-49213000	Weak transcription	Fetal Brain Male	brain
50	chr12:49212200-49213200	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links