Variant report

Variant	rs541109126
Chromosome Location	chr12:48150011-48150012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr12:48149870-48150382	ECC-1	luminal epithelium:	n/a	n/a
2	USF1	chr12:48149795-48150413	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr12:48149889-48150425	ECC-1	luminal epithelium:	n/a	n/a
4	RELA	chr12:48148938-48150083	GM15510	blood:	n/a	n/a
5	ZBTB7A	chr12:48149693-48150562	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr12:48149292-48153761	ECC-1	luminal epithelium:	n/a	chr12:48151904-48151914 chr12:48153083-48153090 chr12:48152062-48152069 chr12:48149639-48149646 chr12:48152628-48152635 chr12:48152630-48152637
7	FOXM1	chr12:48149669-48150520	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr12:48149391-48150410	ECC-1	luminal epithelium:	n/a	n/a
9	EBF1	chr12:48148583-48150102	GM12878	blood:	n/a	chr12:48148786-48148797
10	FOXM1	chr12:48149263-48150609	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr12:48149324-48150627	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr12:48149329-48150589	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr12:48149345-48150590	ECC-1	luminal epithelium:	n/a	n/a
14	EBF1	chr12:48149473-48150056	GM12878	blood:	n/a	n/a
15	RELA	chr12:48148829-48150033	GM19099	blood:	n/a	n/a
16	NR3C1	chr12:48149815-48150336	ECC-1	luminal epithelium:	n/a	n/a
17	NR3C1	chr12:48149890-48150253	ECC-1	luminal epithelium:	n/a	n/a
18	EP300	chr12:48149346-48150555	ECC-1	luminal epithelium:	n/a	n/a
19	RELA	chr12:48148609-48150014	GM18951	blood:	n/a	n/a
20	MAZ	chr12:48149185-48150053	GM12878	blood:	n/a	n/a
21	TEAD4	chr12:48149388-48150456	ECC-1	luminal epithelium:	n/a	n/a
22	TCF12	chr12:48149301-48150594	ECC-1	luminal epithelium:	n/a	chr12:48149639-48149646
23	EP300	chr12:48146839-48150642	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623 chr12:48147400-48147414 chr12:48148703-48148716
24	POLR2A	chr12:48149457-48150397	ECC-1	luminal epithelium:	n/a	n/a
25	USF1	chr12:48149817-48150328	ECC-1	luminal epithelium:	n/a	n/a
26	ESR1	chr12:48149874-48150519	ECC-1	luminal epithelium:	n/a	n/a
27	ESR1	chr12:48149912-48150264	ECC-1	luminal epithelium:	n/a	n/a
28	ESR1	chr12:48149771-48150457	ECC-1	luminal epithelium:	n/a	n/a
29	RUNX3	chr12:48148637-48150045	GM12878	blood:	n/a	chr12:48148819-48148834
30	WRNIP1	chr12:48149813-48150015	GM12878	blood:	n/a	n/a
31	TEAD4	chr12:48149464-48150625	ECC-1	luminal epithelium:	n/a	n/a
32	ESR1	chr12:48149863-48150299	ECC-1	luminal epithelium:	n/a	n/a
33	ZBTB7A	chr12:48149873-48150531	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48149372..48151812-chr12:48213789..48216551,2	MCF-7	breast:
2	chr12:48149008..48151227-chr12:48151474..48154219,4	K562	blood:
3	chr12:48136067..48137625-chr12:48149838..48151816,2	K562	blood:
4	chr12:48148726..48150378-chr12:48297476..48299257,2	MCF-7	breast:
5	chr12:48143654..48145769-chr12:48149480..48151758,2	K562	blood:
6	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-7	chr12:48149485-48150268	NONHSAT027942

No data

Variant related genes	Relation type
SLC48A1	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription 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	78 gene(s)	inside rSNPs	diseases
10	nsv518315	chr12:48149752-48152995	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
4	chr12:48145400-48151400	Enhancers	Placenta	Placenta
5	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:48145600-48151000	Enhancers	Spleen	Spleen
8	chr12:48145800-48151200	Enhancers	Gastric	stomach
9	chr12:48146000-48151400	Enhancers	Stomach Mucosa	stomach
10	chr12:48146200-48150200	Enhancers	Fetal Muscle Leg	muscle
11	chr12:48146600-48150400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr12:48147000-48150400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:48147000-48151800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48147000-48152200	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:48147000-48152400	Enhancers	Primary B cells from cord blood	blood
16	chr12:48147000-48152400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr12:48147200-48150400	Enhancers	Pancreas	Pancrea
18	chr12:48147200-48150800	Enhancers	Ovary	ovary
19	chr12:48147600-48151400	Weak transcription	Fetal Intestine Large	intestine
20	chr12:48147800-48150200	Enhancers	Small Intestine	intestine
21	chr12:48147800-48151400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:48148000-48150200	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr12:48148000-48150800	Enhancers	HUVEC	blood vessel
24	chr12:48148000-48151400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:48148000-48151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:48148000-48151800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:48148000-48152200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:48148200-48150200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:48148200-48151000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:48148200-48151200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:48148200-48151200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:48148200-48151200	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:48148200-48151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:48148200-48151400	Weak transcription	NHLF	lung
35	chr12:48148400-48150200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:48148400-48150200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:48148400-48150800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:48148400-48151200	Weak transcription	NH-A	brain
39	chr12:48148400-48151400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:48148400-48152000	Weak transcription	A549	lung
41	chr12:48148400-48152200	Enhancers	Fetal Thymus	thymus
42	chr12:48148600-48150200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:48148600-48150200	Enhancers	Thymus	Thymus
44	chr12:48148600-48150600	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr12:48148600-48151000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:48148800-48150200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:48148800-48151200	Weak transcription	Fetal Brain Male	brain
48	chr12:48148800-48151200	Weak transcription	Osteobl	bone
49	chr12:48148800-48151400	Active TSS	Stomach Smooth Muscle	stomach
50	chr12:48148800-48151400	Enhancers	HMEC	breast

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