Variant report

Variant	rs12320661
Chromosome Location	chr12:104614491-104614492
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	EP300	chr12:104612319-104614606	A549	lung:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
2	HA-E2F1	chr12:104613709-104614574	MCF-7	breast:	n/a	chr12:104614138-104614147
3	TCF12	chr12:104612668-104615129	A549	lung:	n/a	n/a
4	GATA3	chr12:104612528-104614607	A549	lung:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
5	SP1	chr12:104612572-104614517	A549	lung:	n/a	n/a
6	NR2F2	chr12:104613087-104614503	MCF-7	breast:	n/a	n/a
7	FOXA2	chr12:104613760-104614504	A549	lung:	n/a	chr12:104614084-104614096
8	FOSL2	chr12:104612556-104614709	A549	lung:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
9	SP1	chr12:104612347-104614515	A549	lung:	n/a	n/a
10	SIX5	chr12:104612643-104614957	A549	lung:	n/a	n/a
11	FOXM1	chr12:104612924-104614542	MCF-7	breast:	n/a	n/a
12	TCF12	chr12:104613029-104614626	MCF-7	breast:	n/a	n/a
13	GATA3	chr12:104612902-104614712	MCF-7	breast:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
14	GTF3C2	chr12:104612798-104615011	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104613868..104615389-chr12:104679010..104681119,2	K562	blood:
2	chr12:104611665..104617222-chr12:104678192..104683063,15	MCF-7	breast:
3	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
4	chr12:104612436..104616572-chr12:104617042..104624166,8	MCF-7	breast:
5	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
6	chr12:104613560..104615348-chr12:104617225..104620017,2	MCF-7	breast:
7	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11829922	0.92[EUR][1000 genomes]
rs12303096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12303143	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17807362	0.92[EUR][1000 genomes]
rs57416848	0.92[EUR][1000 genomes]
rs57718153	0.92[EUR][1000 genomes]
rs58729796	0.92[EUR][1000 genomes]
rs59185359	0.84[EUR][1000 genomes]
rs61690515	0.92[EUR][1000 genomes]
rs73392580	0.92[EUR][1000 genomes]
rs73392594	0.92[EUR][1000 genomes]
rs73394503	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73394521	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
2	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104610200-104614800	Weak transcription	Gastric	stomach
2	chr12:104610800-104614800	Weak transcription	Ovary	ovary
3	chr12:104612000-104615400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:104612200-104615000	Enhancers	HMEC	breast
5	chr12:104612200-104617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:104612400-104616400	Enhancers	Placenta	Placenta
7	chr12:104612600-104615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:104612800-104614800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:104612800-104615000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:104612800-104615000	Enhancers	Fetal Stomach	stomach
11	chr12:104613000-104614600	Enhancers	HepG2	liver
12	chr12:104613000-104615600	Enhancers	Stomach Mucosa	stomach
13	chr12:104613000-104616000	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:104613200-104614600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:104613200-104614600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr12:104613400-104614800	Enhancers	Dnd41	blood
17	chr12:104613600-104615000	Enhancers	Left Ventricle	heart
18	chr12:104613800-104615000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:104614000-104614600	Weak transcription	Pancreas	Pancrea
20	chr12:104614000-104614800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:104614000-104614800	Weak transcription	Lung	lung
22	chr12:104614000-104615000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:104614000-104615000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:104614000-104615000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:104614000-104615000	Enhancers	NHDF-Ad	bronchial
26	chr12:104614000-104615000	Enhancers	NHEK	skin
27	chr12:104614000-104616000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:104614000-104616000	Weak transcription	Thymus	Thymus
29	chr12:104614000-104617200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:104614000-104617200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:104614000-104617400	Weak transcription	HSMMtube	muscle
32	chr12:104614000-104619600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:104614000-104623400	Weak transcription	Right Atrium	heart
34	chr12:104614200-104614600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:104614200-104614600	Enhancers	NH-A	brain
36	chr12:104614200-104614800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:104614200-104614800	Weak transcription	Right Ventricle	heart
38	chr12:104614200-104615800	Enhancers	HUVEC	blood vessel
39	chr12:104614200-104615800	Enhancers	NHLF	lung
40	chr12:104614200-104616000	Enhancers	Hela-S3	cervix
41	chr12:104614200-104616600	Weak transcription	Fetal Lung	lung
42	chr12:104614200-104616800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:104614200-104617400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:104614200-104619800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:104614400-104614800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:104614400-104614800	Flanking Active TSS	A549	lung
47	chr12:104614400-104615000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:104614400-104617000	Weak transcription	Fetal Intestine Large	intestine

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