Variant report

Variant	rs139680402
Chromosome Location	chr12:49578419-49578420
allele	-/TG
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49578367-49579450	SK-N-SH	brain:	n/a	n/a
2	REST	chr12:49575982-49579090	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr12:49576928-49578792	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:49578316-49579001	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:49576836-49579887	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr12:49577041-49578970	IMR90	lung:	n/a	n/a
7	POLR2A	chr12:49578335-49579942	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:49576997-49579245	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:49578353-49579001	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49521045..49522741-chr12:49576322..49578574,2	K562	blood:
2	chr12:49523298..49526534-chr12:49578242..49583023,5	K562	blood:
3	chr12:49455381..49457675-chr12:49576315..49579055,2	MCF-7	breast:
4	chr12:49523810..49525846-chr12:49575368..49579813,5	K562	blood:
5	chr12:49577117..49578684-chr12:49582643..49584249,2	K562	blood:

No data

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000167552	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	esv3417605	chr12:49521878-49578961	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
5	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
6	nsv976610	chr12:49577937-49580571	Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49570600-49581000	Weak transcription	GM12878-XiMat	blood
2	chr12:49574200-49578600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:49574200-49580600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:49575200-49578800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:49576000-49578600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:49576000-49580800	Weak transcription	A549	lung
7	chr12:49576200-49578600	Weak transcription	Placenta	Placenta
8	chr12:49576200-49579200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:49576200-49580800	Weak transcription	Fetal Kidney	kidney
10	chr12:49576400-49578600	Weak transcription	Aorta	Aorta
11	chr12:49576400-49578800	Weak transcription	Brain Substantia Nigra	brain
12	chr12:49576400-49578800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:49576400-49580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:49576600-49578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:49576800-49581800	Weak transcription	Liver	Liver
16	chr12:49577000-49578600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:49577000-49578600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:49577000-49579200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:49577000-49579400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:49577000-49580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:49577000-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:49577200-49578600	Genic enhancers	Brain Anterior Caudate	brain
23	chr12:49577200-49578800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:49577200-49578800	Weak transcription	Ovary	ovary
25	chr12:49577200-49578800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:49577200-49580200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:49577200-49580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:49577200-49581000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:49577200-49581000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:49577400-49578600	Genic enhancers	Brain Hippocampus Middle	brain
31	chr12:49577400-49578600	Weak transcription	HSMMtube	muscle
32	chr12:49577400-49579200	Genic enhancers	Brain Inferior Temporal Lobe	brain
33	chr12:49577400-49579800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr12:49577400-49580000	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:49577400-49580200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49577400-49580200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:49577400-49580400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:49577400-49580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:49577400-49580800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:49577400-49581000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:49577400-49581000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:49577400-49581000	Weak transcription	Colonic Mucosa	Colon
43	chr12:49577400-49581000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:49577400-49581800	Weak transcription	Pancreas	Pancrea
45	chr12:49577400-49581800	Weak transcription	Small Intestine	intestine
46	chr12:49577600-49578600	Weak transcription	NHLF	lung
47	chr12:49577600-49578800	Genic enhancers	Brain Cingulate Gyrus	brain
48	chr12:49577600-49579400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:49577600-49579600	Strong transcription	HSMM	muscle
50	chr12:49577600-49579800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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