Variant report

Variant	rs577902991
Chromosome Location	chr12:4388756-4388757
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	POLR2A	chr12:4378383-4393977	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:4385965-4389349	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:4385697-4406476	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:4386676-4402492	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr12:4388589-4388874	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:4377522-4393821	GM19099	blood:	n/a	n/a
7	POLR2A	chr12:4384783-4393854	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:4388672-4391133	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr12:4377597-4393888	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:4388548-4388863	GM12892	blood:	n/a	n/a
11	WRNIP1	chr12:4388645-4389569	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:4388513-4400468	GM19193	blood:	n/a	n/a
13	POLR2A	chr12:4388751-4389934	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:4388618-4393839	GM18526	blood:	n/a	n/a
15	POLR2A	chr12:4377513-4404672	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:4385126-4393865	K562	blood:	n/a	n/a
17	POLR2A	chr12:4388436-4393945	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:4388506-4391070	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:4388414-4408317	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CCND2-AS1	TF binding region
CCND2-AS2	TF binding region

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

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541360	chr12:4338851-4389238	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv541361	chr12:4362258-4413849	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv275292	chr12:4388532-4389337	Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3482051	chr12:4388628-4389430	Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3482040	chr12:4388682-4389407	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3482075	chr12:4388691-4389400	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3482064	chr12:4388695-4389358	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv826196	chr12:4388696-4389213	Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv826197	chr12:4388723-4389213	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv826199	chr12:4388757-4389213	Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 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	chr12:4384400-4390600	Weak transcription	Gastric	stomach
2	chr12:4385000-4390000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
3	chr12:4385200-4390800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:4385200-4390800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr12:4385200-4391000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
6	chr12:4385400-4388800	Genic enhancers	Primary hematopoietic stem cells	blood
7	chr12:4385400-4400000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
8	chr12:4385400-4404400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
9	chr12:4385600-4389400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:4385600-4389600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
11	chr12:4385600-4390000	Genic enhancers	HSMM	muscle
12	chr12:4385600-4390400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:4385600-4390600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:4385600-4390800	Genic enhancers	Colonic Mucosa	Colon
15	chr12:4385600-4390800	Genic enhancers	Fetal Lung	lung
16	chr12:4385600-4391000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:4385600-4391400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:4385600-4400600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:4385800-4390400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:4385800-4390600	Genic enhancers	Placenta Amnion	Placenta Amnion
21	chr12:4385800-4398400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:4386000-4390200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:4386000-4393600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:4386000-4400000	Genic enhancers	Fetal Stomach	stomach
25	chr12:4386000-4404600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr12:4386200-4389200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:4386200-4389600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr12:4386200-4389600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:4386200-4390200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:4386200-4390400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:4386200-4390800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:4386200-4393200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:4386200-4403000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:4386200-4404200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr12:4386200-4404800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:4386400-4389000	Genic enhancers	Rectal Smooth Muscle	rectum
37	chr12:4386400-4393800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:4386600-4389200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:4386600-4389600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:4386600-4389800	Genic enhancers	NHEK	skin
41	chr12:4386600-4390200	Genic enhancers	Colon Smooth Muscle	Colon
42	chr12:4386600-4390600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:4386600-4390800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:4386600-4393200	Weak transcription	Brain Substantia Nigra	brain
45	chr12:4386600-4393200	Weak transcription	Thymus	Thymus
46	chr12:4386600-4395000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:4386600-4400000	Genic enhancers	Fetal Muscle Leg	muscle
48	chr12:4386600-4406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:4386800-4389000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:4386800-4391800	Genic enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links