Variant report

Variant	rs12307969
Chromosome Location	chr12:46759057-46759058
allele	C/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	chr12:46754898-46760301	U87	brain:	n/a	n/a
2	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
3	POLR2A	chr12:46758700-46760175	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:46757569-46760144	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
7	MXI1	chr12:46758733-46759364	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:46758728-46760155	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:46758723-46760310	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:46758790-46759196	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
14	RAD21	chr12:46759055-46759363	IMR90	lung:	n/a	n/a
15	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
16	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
17	NFIC	chr12:46758851-46759416	HepG2	liver:	n/a	chr12:46759202-46759230
18	JUND	chr12:46758678-46760244	SK-N-SH	brain:	n/a	n/a
19	FOSL2	chr12:46758812-46759414	A549	lung:	n/a	n/a
20	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
21	EP300	chr12:46759020-46759337	SK-N-SH_RA	brain:	n/a	n/a
22	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr12:46758771-46759381	SK-N-MC	brain:	n/a	n/a
24	EBF1	chr12:46758672-46759327	GM12878	blood:	n/a	n/a
25	E2F4	chr12:46758960-46759340	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:46758988-46759116	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
28	NFIC	chr12:46758778-46759727	SK-N-SH	brain:	n/a	chr12:46759202-46759230
29	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
30	POLR2A	chr12:46758684-46767978	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr12:46758924-46759620	ECC-1	luminal epithelium:	n/a	chr12:46759202-46759230
32	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
33	GATA3	chr12:46758922-46760195	A549	lung:	n/a	chr12:46759305-46759312 chr12:46759305-46759312 chr12:46759298-46759319 chr12:46759305-46759314 chr12:46759305-46759312
34	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
35	MBD4	chr12:46756528-46760338	HepG2	liver:	n/a	n/a
36	ATF2	chr12:46758645-46759470	GM12878	blood:	n/a	n/a
37	FOSL1	chr12:46758894-46759562	HCT-116	colon:	n/a	n/a
38	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
39	POLR2A	chr12:46758842-46759354	ProgFib	skin:	n/a	n/a
40	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
42	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
43	POLR2A	chr12:46758649-46760326	PANC-1	pancreas:	n/a	n/a
44	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
45	NFIC	chr12:46758604-46759493	GM12878	blood:	n/a	chr12:46759202-46759230 chr12:46758741-46758769
46	IKZF1	chr12:46758788-46759229	GM12878	blood:	n/a	n/a
47	RUNX3	chr12:46758746-46759125	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:46758717-46759401	SK-N-SH	brain:	n/a	n/a
49	CUX1	chr12:46758947-46759361	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:46759019-46759293	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
2	chr12:46658898..46664029-chr12:46756711..46760586,4	K562	blood:

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10785620	0.92[EUR][1000 genomes]
rs10785624	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880962	0.87[EUR][1000 genomes]
rs12296120	0.93[EUR][1000 genomes]
rs12320197	0.94[EUR][1000 genomes]
rs1873793	0.98[EUR][1000 genomes]
rs2279559	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35377637	0.88[EUR][1000 genomes]
rs7972573	0.82[EUR][1000 genomes]

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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46737600-46761200	Weak transcription	Gastric	stomach
2	chr12:46744000-46760600	Weak transcription	Spleen	Spleen
3	chr12:46748800-46764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:46750400-46761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:46751600-46760600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:46751600-46761200	Strong transcription	Fetal Brain Female	brain
7	chr12:46751800-46759200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:46752200-46761200	Strong transcription	Placenta	Placenta
9	chr12:46752400-46759800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:46752400-46760400	Strong transcription	Brain Germinal Matrix	brain
11	chr12:46752400-46761400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:46752400-46761600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:46752400-46761600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:46752400-46761800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:46752600-46759200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:46752600-46759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:46752600-46760600	Strong transcription	Fetal Thymus	thymus
19	chr12:46752600-46761200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr12:46752600-46761200	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:46752600-46761400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr12:46752600-46761600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:46752800-46759400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:46752800-46759600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:46752800-46760600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:46752800-46761200	Strong transcription	Left Ventricle	heart
31	chr12:46752800-46761600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:46752800-46762000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:46753000-46761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:46753000-46762600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:46753200-46760400	Weak transcription	Fetal Stomach	stomach
36	chr12:46753200-46761000	Strong transcription	Fetal Kidney	kidney
37	chr12:46753400-46761200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr12:46753400-46761800	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:46753400-46762400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:46753600-46761200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:46753600-46761600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:46754000-46759800	Weak transcription	Pancreas	Pancrea
45	chr12:46754000-46761200	Genic enhancers	Primary T cells from cord blood	blood
46	chr12:46754000-46761200	Weak transcription	Esophagus	oesophagus
47	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:46754600-46762600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
50	chr12:46754800-46759800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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