Variant report

Variant	rs12713287
Chromosome Location	chr2:55343615-55343616
allele	A/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	TAL1	chr2:55343223-55343639	K562	blood:	n/a	n/a
2	JUN	chr2:55342894-55343863	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
3	CEBPD	chr2:55343111-55343727	K562	blood:	n/a	n/a
4	SP1	chr2:55342679-55343706	HCT-116	colon:	n/a	chr2:55342792-55342805
5	CEBPB	chr2:55343117-55343651	K562	blood:	n/a	n/a
6	JUN	chr2:55342362-55344019	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
7	TCF12	chr2:55342683-55343679	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr2:55342716-55343653	SK-N-SH	brain:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
9	JUND	chr2:55342698-55343713	HCT-116	colon:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
10	JUND	chr2:55342457-55343976	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
11	CEBPB	chr2:55342698-55343784	HCT-116	colon:	n/a	n/a
12	TBL1XR1	chr2:55342886-55343870	K562	blood:	n/a	n/a
13	GATA3	chr2:55342523-55343757	SK-N-SH	brain:	n/a	chr2:55343402-55343414 chr2:55343403-55343412 chr2:55342694-55342710
14	BHLHE40	chr2:55343380-55343848	K562	blood:	n/a	n/a
15	GATA2	chr2:55343197-55343632	K562	blood:	n/a	chr2:55343402-55343414 chr2:55343403-55343412
16	FOSL1	chr2:55342623-55343669	HCT-116	colon:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343342-55343353 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
17	TEAD4	chr2:55342694-55343719	K562	blood:	n/a	n/a
18	CCNT2	chr2:55343202-55343687	K562	blood:	n/a	n/a
19	FOSL1	chr2:55342721-55343688	HCT-116	colon:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343342-55343353 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
20	HMGN3	chr2:55343193-55343671	K562	blood:	n/a	n/a
21	ARID3A	chr2:55343213-55343825	K562	blood:	n/a	n/a
22	CEBPD	chr2:55343259-55343677	K562	blood:	n/a	n/a
23	CEBPB	chr2:55342734-55343724	HCT-116	colon:	n/a	n/a
24	GATA1	chr2:55343052-55343860	PBDE	blood:	n/a	chr2:55343402-55343414 chr2:55343403-55343412
25	EP300	chr2:55342333-55343813	K562	blood:	n/a	chr2:55343036-55343045
26	CUX1	chr2:55343254-55343886	K562	blood:	n/a	chr2:55343495-55343509
27	ZMIZ1	chr2:55342999-55343849	K562	blood:	n/a	n/a
28	MAFK	chr2:55342845-55343656	K562	blood:	n/a	chr2:55343029-55343045 chr2:55343034-55343043 chr2:55343029-55343044
29	RCOR1	chr2:55342434-55344020	K562	blood:	n/a	n/a
30	JUND	chr2:55342775-55343663	HCT-116	colon:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
31	JUND	chr2:55342314-55344001	SK-N-SH	brain:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
32	SP1	chr2:55342616-55343826	HCT-116	colon:	n/a	chr2:55342792-55342805
33	EP300	chr2:55342879-55343645	Hela-S3	cervix:	n/a	chr2:55343036-55343045
34	GATA1	chr2:55341662-55344054	K562	blood:	n/a	chr2:55343402-55343414 chr2:55343403-55343412 chr2:55342694-55342710
35	TEAD4	chr2:55342845-55343658	K562	blood:	n/a	n/a
36	JUN	chr2:55342863-55343615	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
37	POLR2A	chr2:55342739-55343695	U87	brain:	n/a	n/a
38	FOS	chr2:55342902-55343673	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343034-55343045 chr2:55343036-55343044 chr2:55343035-55343045

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55343511..55346556-chr2:55364762..55366710,3	K562	blood:
3	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
4	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
5	chr2:55341952..55344762-chr2:55357897..55359885,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10168457	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10496039	0.90[ASN][1000 genomes]
rs11681508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692696	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990261	0.82[ASN][1000 genomes]
rs13006159	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:55338600-55343800	Enhancers	Fetal Muscle Leg	muscle
3	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
9	chr2:55339800-55344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55339800-55345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:55339800-55345800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:55339800-55347000	Weak transcription	Lung	lung
13	chr2:55340000-55345600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:55340200-55346200	Weak transcription	Fetal Brain Female	brain
15	chr2:55340400-55344200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:55340400-55345800	Enhancers	K562	blood
17	chr2:55340600-55344400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:55340600-55345200	Weak transcription	Fetal Brain Male	brain
19	chr2:55340600-55347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:55340800-55343800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:55340800-55344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:55340800-55345600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:55340800-55346000	Weak transcription	Spleen	Spleen
24	chr2:55340800-55347200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:55340800-55348000	Enhancers	Brain Hippocampus Middle	brain
26	chr2:55340800-55348000	Enhancers	Brain Substantia Nigra	brain
27	chr2:55341000-55345800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:55341000-55346000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:55341000-55346800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:55341000-55346800	Weak transcription	Placenta	Placenta
31	chr2:55341200-55344400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:55341200-55345600	Weak transcription	Primary B cells from cord blood	blood
33	chr2:55341200-55345800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:55341200-55346200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:55341200-55346800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:55341200-55347000	Weak transcription	Stomach Mucosa	stomach
37	chr2:55341400-55345800	Weak transcription	Adipose Nuclei	Adipose
38	chr2:55341600-55345800	Weak transcription	Fetal Thymus	thymus
39	chr2:55341800-55344400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:55341800-55344600	Enhancers	NHDF-Ad	bronchial
41	chr2:55342000-55343800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:55342000-55343800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:55342200-55346200	Enhancers	Hela-S3	cervix
44	chr2:55342200-55347000	Enhancers	HSMMtube	muscle
45	chr2:55342400-55350200	Enhancers	Fetal Heart	heart
46	chr2:55342600-55344000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:55342600-55344600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:55342600-55344600	Enhancers	NHEK	skin
49	chr2:55342800-55344200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:55343000-55344600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links