Variant report

Variant	rs55698768
Chromosome Location	chr12:46758376-46758377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

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	chr12:46758220-46758603	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:46757400-46758422	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr12:46757402-46758483	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:46757569-46760144	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:46757716-46758526	SK-N-SH	brain:	n/a	n/a
13	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
14	POLR2A	chr12:46754389-46758566	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr12:46758357-46758634	K562	blood:	n/a	n/a
17	POLR2A	chr12:46758007-46758413	HCT-116	colon:	n/a	n/a
18	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr12:46757399-46758616	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
22	MAZ	chr12:46758355-46758450	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:46757971-46758537	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
25	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
26	MBD4	chr12:46756528-46760338	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
28	SP1	chr12:46758037-46758475	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
30	POLR2A	chr12:46756506-46758577	HepG2	liver:	n/a	n/a
31	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
32	POLR2A	chr12:46757502-46758505	PFSK-1	brain:	n/a	n/a
33	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
34	MYBL2	chr12:46757993-46758601	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:46757395-46758617	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:46754307-46767479	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr12:46750204-46767088	U87	brain:	n/a	n/a
38	POLR2A	chr12:46758041-46758439	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr12:46750335-46767686	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:46758339-46758549	K562	blood:	n/a	n/a
41	POLR2A	chr12:46756541-46758619	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:46757417-46758502	K562	blood:	n/a	n/a
43	POLR2A	chr12:46750216-46767088	U87	brain:	n/a	n/a
44	POLR2A	chr12:46757706-46758784	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:46750303-46767380	U87	brain:	n/a	n/a
46	POLR2A	chr12:46757560-46764323	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46756844..46758445-chr12:46930645..46932829,2	K562	blood:
2	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
3	chr12:46658898..46664029-chr12:46756711..46760586,4	K562	blood:

No data

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000272369	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11830080	1.00[AMR][1000 genomes]
rs11830086	1.00[AMR][1000 genomes]
rs11837634	1.00[AMR][1000 genomes]
rs17096996	1.00[AMR][1000 genomes]
rs2085682	1.00[AMR][1000 genomes]
rs2408578	1.00[AMR][1000 genomes]
rs55649919	1.00[AMR][1000 genomes]
rs56160202	1.00[AMR][1000 genomes]
rs59451063	1.00[AMR][1000 genomes]
rs7136748	1.00[AMR][1000 genomes]
rs74081912	1.00[AMR][1000 genomes]
rs74082033	1.00[AMR][1000 genomes]
rs74082237	1.00[AMR][1000 genomes]
rs74082263	1.00[AMR][1000 genomes]
rs74082274	1.00[AMR][1000 genomes]
rs74083751	1.00[AMR][1000 genomes]
rs74083758	1.00[AMR][1000 genomes]
rs74085404	1.00[AMR][1000 genomes]
rs74085421	1.00[AMR][1000 genomes]
rs74085432	1.00[AMR][1000 genomes]
rs74085442	1.00[AMR][1000 genomes]
rs7975472	1.00[AMR][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	chr12:46752400-46758600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr12:46752400-46759000	Strong transcription	Colonic Mucosa	Colon
11	chr12:46752400-46759800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:46752400-46760400	Strong transcription	Brain Germinal Matrix	brain
13	chr12:46752400-46761400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:46752400-46761600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:46752400-46761600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:46752400-46761800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:46752600-46758800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:46752600-46758800	Strong transcription	Fetal Intestine Large	intestine
20	chr12:46752600-46758800	Strong transcription	NH-A	brain
21	chr12:46752600-46759000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:46752600-46759000	Strong transcription	Fetal Lung	lung
23	chr12:46752600-46759200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:46752600-46759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:46752600-46760600	Strong transcription	Fetal Thymus	thymus
26	chr12:46752600-46761200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:46752600-46761200	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:46752600-46761400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:46752600-46761600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr12:46752800-46759000	Strong transcription	HSMMtube	muscle
35	chr12:46752800-46759400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:46752800-46759600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:46752800-46760600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:46752800-46761200	Strong transcription	Left Ventricle	heart
39	chr12:46752800-46761600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:46752800-46762000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:46753000-46758800	Strong transcription	K562	blood
42	chr12:46753000-46761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:46753000-46762600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:46753200-46760400	Weak transcription	Fetal Stomach	stomach
45	chr12:46753200-46761000	Strong transcription	Fetal Kidney	kidney
46	chr12:46753400-46758800	Weak transcription	Fetal Intestine Small	intestine
47	chr12:46753400-46761200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr12:46753400-46761800	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:46753400-46762400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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