Variant report

Variant	rs56357425
Chromosome Location	chr12:121419089-121419090
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	HEY1	chr12:121415737-121419289	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:121415550-121419599	HepG2	liver:	n/a	n/a
3	FOXA2	chr12:121418450-121419985	A549	lung:	n/a	n/a
4	FOXA1	chr12:121418464-121419924	HepG2	liver:	n/a	n/a
5	CEBPD	chr12:121418459-121419167	HepG2	liver:	n/a	n/a
6	SP1	chr12:121417828-121419896	A549	lung:	n/a	chr12:121418655-121418664 chr12:121418414-121418428 chr12:121418308-121418317 chr12:121418127-121418134 chr12:121418964-121418976 chr12:121419279-121419293 chr12:121418966-121418975 chr12:121418654-121418666 chr12:121418307-121418316 chr12:121418965-121418974 chr12:121418420-121418434 chr12:121418654-121418666 chr12:121418656-121418665 chr12:121418961-121418975 chr12:121418358-121418370 chr12:121418235-121418249 chr12:121418655-121418665 chr12:121418719-121418733 chr12:121418964-121418976 chr12:121418651-121418665 chr12:121418360-121418369
7	MAX	chr12:121418544-121419905	A549	lung:	n/a	n/a
8	POLR2A	chr12:121415325-121419806	HepG2	liver:	n/a	n/a
9	GATA3	chr12:121418439-121419878	A549	lung:	n/a	n/a
10	BCL3	chr12:121418529-121419864	A549	lung:	n/a	chr12:121418966-121418975 chr12:121418656-121418665
11	TCF12	chr12:121417737-121419987	A549	lung:	n/a	n/a
12	POLR2A	chr12:121418883-121419104	HepG2	liver:	n/a	n/a
13	EP300	chr12:121417762-121419990	A549	lung:	n/a	chr12:121417810-121417826
14	FOXA2	chr12:121418430-121419872	HepG2	liver:	n/a	n/a
15	BCL3	chr12:121418508-121419849	A549	lung:	n/a	chr12:121418966-121418975 chr12:121418656-121418665
16	FOXA2	chr12:121417957-121419962	A549	lung:	n/a	n/a
17	MAX	chr12:121415630-121419965	A549	lung:	n/a	chr12:121416508-121416515 chr12:121416545-121416554 chr12:121418418-121418428 chr12:121416195-121416205
18	REST	chr12:121416814-121419966	A549	lung:	n/a	chr12:121417024-121417033 chr12:121418415-121418428 chr12:121418147-121418156 chr12:121417597-121417617 chr12:121416921-121416934 chr12:121418828-121418836 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162 chr12:121416912-121416925
19	SP1	chr12:121417899-121419116	HepG2	liver:	n/a	chr12:121418655-121418664 chr12:121418414-121418428 chr12:121418308-121418317 chr12:121418127-121418134 chr12:121418964-121418976 chr12:121418966-121418975 chr12:121418654-121418666 chr12:121418307-121418316 chr12:121418965-121418974 chr12:121418420-121418434 chr12:121418654-121418666 chr12:121418656-121418665 chr12:121418961-121418975 chr12:121418358-121418370 chr12:121418235-121418249 chr12:121418655-121418665 chr12:121418719-121418733 chr12:121418964-121418976 chr12:121418651-121418665 chr12:121418360-121418369
20	POLR2A	chr12:121414963-121419793	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:121417761-121419499	HepG2	liver:	n/a	n/a
22	EP300	chr12:121417782-121419907	A549	lung:	n/a	chr12:121417810-121417826
23	MYBL2	chr12:121417881-121419136	HepG2	liver:	n/a	n/a
24	FOSL2	chr12:121417804-121419089	A549	lung:	n/a	chr12:121418094-121418106 chr12:121418654-121418663
25	MYBL2	chr12:121418366-121419760	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:121418850-121419201	HepG2	liver:	n/a	n/a
27	SP1	chr12:121417754-121419928	A549	lung:	n/a	chr12:121418655-121418664 chr12:121418414-121418428 chr12:121418308-121418317 chr12:121418127-121418134 chr12:121417754-121417768 chr12:121418964-121418976 chr12:121419279-121419293 chr12:121418966-121418975 chr12:121418654-121418666 chr12:121418307-121418316 chr12:121418965-121418974 chr12:121418420-121418434 chr12:121418654-121418666 chr12:121418656-121418665 chr12:121418961-121418975 chr12:121418358-121418370 chr12:121418235-121418249 chr12:121418655-121418665 chr12:121418719-121418733 chr12:121417765-121417775 chr12:121418964-121418976 chr12:121418651-121418665 chr12:121418360-121418369
28	HEY1	chr12:121417763-121419825	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121410040..121412493-chr12:121417620..121420402,3	MCF-7	breast:

Variant related genes	Relation type
HNF1A-AS1	TF binding region
ENSG00000272214	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11537856	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1169293	1.00[ASN][1000 genomes]
rs2245407	1.00[ASN][1000 genomes]
rs2393795	1.00[AFR][1000 genomes]
rs3213547	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41279100	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55660034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55811663	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55961602	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56046951	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56280478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56298275	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56360386	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61953351	1.00[ASN][1000 genomes]
rs73214128	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214130	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214134	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214136	1.00[AFR][1000 genomes]
rs73214141	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214143	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73224338	1.00[AFR][1000 genomes]
rs73224341	1.00[AFR][1000 genomes]
rs73224342	1.00[AFR][1000 genomes]
rs73226260	0.83[AMR][1000 genomes]
rs73226262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73226263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73226267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73226273	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73226287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73226288	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73226292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:121415400-121419200	Active TSS	Fetal Kidney	kidney
3	chr12:121415400-121419800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:121416000-121419200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:121417800-121419600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:121418000-121420000	Flanking Active TSS	A549	lung
7	chr12:121418200-121419200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:121418200-121421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:121418600-121419200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:121418600-121421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:121418600-121422000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:121418600-121422200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:121418600-121441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:121418800-121419200	Flanking Active TSS	Pancreas	Pancrea
15	chr12:121418800-121419400	Flanking Active TSS	Liver	Liver
16	chr12:121418800-121421600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:121418800-121422200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:121418800-121422200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:121418800-121422200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:121418800-121431800	Weak transcription	Fetal Stomach	stomach
21	chr12:121418800-121439400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:121419000-121419200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr12:121419000-121419200	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr12:121419000-121419200	Enhancers	Stomach Mucosa	stomach
25	chr12:121419000-121419400	Enhancers	Fetal Lung	lung
26	chr12:121419000-121419400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:121419000-121419600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
28	chr12:121419000-121419600	Flanking Active TSS	HepG2	liver
29	chr12:121419000-121419800	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr12:121419000-121419800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:121419000-121421200	Enhancers	Gastric	stomach
32	chr12:121419000-121422000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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