Variant report

Variant	rs10848543
Chromosome Location	chr12:1769930-1769931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:1769290-1770071	MCF10A-Er-Src	breast:	n/a	chr12:1769577-1769587
2	CEBPB	chr12:1769279-1769956	HCT-116	colon:	n/a	n/a
3	TCF7L2	chr12:1769392-1770000	Hela-S3	cervix:	n/a	n/a
4	USF2	chr12:1769181-1770023	Hela-S3	cervix:	n/a	chr12:1769577-1769588
5	MYC	chr12:1769168-1769954	MCF10A-Er-Src	breast:	n/a	chr12:1769577-1769587
6	RAD21	chr12:1769387-1769969	Hela-S3	cervix:	n/a	n/a
7	TBP	chr12:1769225-1770105	Hela-S3	cervix:	n/a	n/a
8	EP300	chr12:1769361-1770135	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr12:1769466-1770022	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr12:1769394-1770043	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr12:1769463-1770047	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr12:1769479-1769943	MCF10A-Er-Src	breast:	n/a	n/a
13	RFX5	chr12:1769247-1770149	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr12:1769441-1770121	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:1768890-1771564	Hela-S3	cervix:	n/a	n/a
16	CREB1	chr12:1769301-1769936	HepG2	liver:	n/a	n/a
17	GTF2F1	chr12:1769341-1770024	Hela-S3	cervix:	n/a	n/a
18	SMC3	chr12:1769355-1769990	Hela-S3	cervix:	n/a	n/a
19	HEY1	chr12:1769325-1770023	HepG2	liver:	n/a	n/a
20	CEBPB	chr12:1769299-1770103	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:1769335-1770177	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr12:1769263-1770028	Hela-S3	cervix:	n/a	n/a
23	MXI1	chr12:1769409-1770053	Hela-S3	cervix:	n/a	n/a
24	JUND	chr12:1769370-1770020	Hela-S3	cervix:	n/a	chr12:1769575-1769584
25	POLR2A	chr12:1769287-1770111	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr12:1769263-1770021	HCT-116	colon:	n/a	n/a
27	SP1	chr12:1769283-1769973	HCT-116	colon:	n/a	n/a
28	E2F4	chr12:1769527-1769995	MCF10A-Er-Src	breast:	n/a	n/a
29	MAX	chr12:1769332-1770072	Hela-S3	cervix:	n/a	chr12:1769577-1769587
30	CHD2	chr12:1769322-1770028	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:1769818..1772528-chr12:1789216..1791447,2	MCF-7	breast:
2	chr12:1769575..1772464-chr12:1879364..1881156,2	MCF-7	breast:
3	chr12:1713956..1716010-chr12:1769729..1772627,2	K562	blood:
4	chr12:1768367..1774746-chr12:1797764..1801789,11	MCF-7	breast:
5	chr12:1769759..1773174-chr12:1808605..1811319,4	K562	blood:
6	chr12:1769387..1773191-chr12:1797591..1801415,7	K562	blood:
7	chr12:1714073..1716320-chr12:1769729..1772377,3	K562	blood:
8	chr12:1769849..1773599-chr12:1775643..1780093,7	K562	blood:
9	chr12:1727058..1729024-chr12:1769642..1771498,2	K562	blood:
10	chr12:1769631..1770598-chr12:130611123..130611927,2	Hela-S3	cervix:
11	chr12:1769374..1771394-chr12:1903241..1905339,2	K562	blood:
12	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:

No data

Variant related genes	Relation type
MIR3649	TF binding region
ENSG00000151062	Chromatin interaction
ENSG00000006831	Chromatin interaction

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

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

rs_ID	r²[population]
rs10773977	0.81[EUR][1000 genomes]
rs10848546	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11615883	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36115201	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489319	0.90[CEU][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs7301222	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv468964	chr12:1749905-1769930	Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv556995	chr12:1749905-1769930	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1754200-1770600	Weak transcription	Colonic Mucosa	Colon
2	chr12:1758000-1770800	Weak transcription	HSMMtube	muscle
3	chr12:1758400-1770600	Weak transcription	NH-A	brain
4	chr12:1759800-1770600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:1760000-1770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:1760200-1770600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:1760800-1770800	Weak transcription	HSMM	muscle
8	chr12:1761400-1770800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:1761600-1770800	Weak transcription	NHLF	lung
10	chr12:1764400-1770600	Weak transcription	Osteobl	bone
11	chr12:1764800-1770800	Weak transcription	NHDF-Ad	bronchial
12	chr12:1765000-1770200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:1767800-1770600	Enhancers	Fetal Intestine Large	intestine
14	chr12:1768200-1770000	Enhancers	Fetal Intestine Small	intestine
15	chr12:1768400-1770000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:1768600-1770600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:1768600-1770600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:1768800-1770000	Enhancers	Lung	lung
19	chr12:1768800-1770600	Enhancers	Pancreas	Pancrea
20	chr12:1768800-1770800	Enhancers	Stomach Mucosa	stomach
21	chr12:1769000-1770000	Enhancers	Liver	Liver
22	chr12:1769000-1770000	Enhancers	Fetal Stomach	stomach
23	chr12:1769000-1770200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr12:1769000-1770400	Enhancers	Fetal Muscle Leg	muscle
25	chr12:1769000-1770600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:1769000-1770600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:1769000-1770600	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:1769000-1770600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:1769000-1770600	Enhancers	HMEC	breast
30	chr12:1769000-1770800	Enhancers	HUVEC	blood vessel
31	chr12:1769000-1771000	Enhancers	K562	blood
32	chr12:1769000-1771400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:1769200-1770000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:1769200-1770000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:1769200-1770000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:1769200-1770000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:1769200-1770200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:1769200-1770400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:1769200-1770600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:1769200-1770600	Weak transcription	Psoas Muscle	Psoas
41	chr12:1769200-1770600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr12:1769200-1770600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:1769200-1770600	Weak transcription	Right Ventricle	heart
44	chr12:1769200-1771400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:1769400-1770000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:1769400-1770000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr12:1769400-1770000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:1769400-1770000	Enhancers	Brain Germinal Matrix	brain
49	chr12:1769400-1770000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr12:1769400-1770000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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