Variant report

Variant	rs553437355
Chromosome Location	chr12:48149796-48149797
allele	C/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	USF1	chr12:48149795-48150413	ECC-1	luminal epithelium:	n/a	n/a
2	RUNX3	chr12:48148641-48149985	GM12878	blood:	n/a	chr12:48148819-48148834
3	TBL1XR1	chr12:48149247-48149971	GM12878	blood:	n/a	n/a
4	NFIC	chr12:48148793-48149999	GM12878	blood:	n/a	n/a
5	MTA3	chr12:48148435-48149970	GM12878	blood:	n/a	n/a
6	RELA	chr12:48148938-48150083	GM15510	blood:	n/a	n/a
7	ZBTB7A	chr12:48149693-48150562	ECC-1	luminal epithelium:	n/a	n/a
8	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
9	FOXM1	chr12:48149669-48150520	ECC-1	luminal epithelium:	n/a	n/a
10	ATF2	chr12:48149153-48149953	GM12878	blood:	n/a	n/a
11	EP300	chr12:48148642-48149887	GM12878	blood:	n/a	chr12:48148703-48148716
12	MAX	chr12:48149391-48150410	ECC-1	luminal epithelium:	n/a	n/a
13	RCOR1	chr12:48148741-48149903	GM12878	blood:	n/a	n/a
14	EBF1	chr12:48148583-48150102	GM12878	blood:	n/a	chr12:48148786-48148797
15	FOXM1	chr12:48149263-48150609	ECC-1	luminal epithelium:	n/a	n/a
16	STAT1	chr12:48149676-48149908	GM12878	blood:	n/a	n/a
17	NFIC	chr12:48149324-48150627	ECC-1	luminal epithelium:	n/a	n/a
18	NFIC	chr12:48149329-48150589	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr12:48149345-48150590	ECC-1	luminal epithelium:	n/a	n/a
20	EBF1	chr12:48149473-48150056	GM12878	blood:	n/a	n/a
21	RELA	chr12:48148829-48150033	GM19099	blood:	n/a	n/a
22	EP300	chr12:48149346-48150555	ECC-1	luminal epithelium:	n/a	n/a
23	RELA	chr12:48148609-48150014	GM18951	blood:	n/a	n/a
24	MAZ	chr12:48149185-48150053	GM12878	blood:	n/a	n/a
25	TEAD4	chr12:48149388-48150456	ECC-1	luminal epithelium:	n/a	n/a
26	TCF12	chr12:48149301-48150594	ECC-1	luminal epithelium:	n/a	chr12:48149639-48149646
27	EP300	chr12:48146839-48150642	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623 chr12:48147400-48147414 chr12:48148703-48148716
28	POLR2A	chr12:48149457-48150397	ECC-1	luminal epithelium:	n/a	n/a
29	ELF1	chr12:48149456-48149862	GM12878	blood:	n/a	n/a
30	MTA3	chr12:48149192-48149807	GM12878	blood:	n/a	n/a
31	ESR1	chr12:48149771-48150457	ECC-1	luminal epithelium:	n/a	n/a
32	RUNX3	chr12:48148637-48150045	GM12878	blood:	n/a	chr12:48148819-48148834
33	TEAD4	chr12:48149464-48150625	ECC-1	luminal epithelium:	n/a	n/a
34	PML	chr12:48148668-48149909	GM12878	blood:	n/a	n/a

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	chr12:48148726..48150378-chr12:48297476..48299257,2	MCF-7	breast:
4	chr12:48143654..48145769-chr12:48149480..48151758,2	K562	blood:
5	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:

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

Variant related genes	Relation type
SLC48A1	TF binding region
RAPGEF3	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
5	chr12:48145400-48151400	Enhancers	Placenta	Placenta
6	chr12:48145600-48149800	Enhancers	HSMMtube	muscle
7	chr12:48145600-48150000	Enhancers	Fetal Muscle Trunk	muscle
8	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:48145600-48151000	Enhancers	Spleen	Spleen
11	chr12:48145800-48151200	Enhancers	Gastric	stomach
12	chr12:48146000-48151400	Enhancers	Stomach Mucosa	stomach
13	chr12:48146200-48150200	Enhancers	Fetal Muscle Leg	muscle
14	chr12:48146600-48150400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:48147000-48150400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:48147000-48151800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:48147000-48152200	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:48147000-48152400	Enhancers	Primary B cells from cord blood	blood
19	chr12:48147000-48152400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr12:48147200-48150400	Enhancers	Pancreas	Pancrea
21	chr12:48147200-48150800	Enhancers	Ovary	ovary
22	chr12:48147600-48150000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48147600-48150000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:48147600-48151400	Weak transcription	Fetal Intestine Large	intestine
25	chr12:48147800-48149800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:48147800-48150000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:48147800-48150200	Enhancers	Small Intestine	intestine
28	chr12:48147800-48151400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:48148000-48150200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr12:48148000-48150800	Enhancers	HUVEC	blood vessel
31	chr12:48148000-48151400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:48148000-48151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:48148000-48151800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr12:48148000-48152200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:48148200-48149800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:48148200-48149800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:48148200-48150000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:48148200-48150200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:48148200-48151000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:48148200-48151200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:48148200-48151200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:48148200-48151200	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:48148200-48151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:48148200-48151400	Weak transcription	NHLF	lung
45	chr12:48148400-48149800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:48148400-48150000	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:48148400-48150200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:48148400-48150200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:48148400-48150800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:48148400-48151200	Weak transcription	NH-A	brain

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