Variant report

Variant	rs558408386
Chromosome Location	chr12:1929414-1929415
allele	-/AGGGGA
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	SIN3A	chr12:1929361-1929809	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:1929345-1929675	HL-60	blood:	n/a	n/a
3	MXI1	chr12:1928518-1930411	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:1929349-1929915	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
LRTM2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
4	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS 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 target site	16 gene(s)	inside rSNPs	diseases
5	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv468965	chr12:1907853-1931396	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556997	chr12:1907853-1931396	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv468966	chr12:1907853-1933553	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv556998	chr12:1907853-1933553	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470259	chr12:1907853-1945042	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv518013	chr12:1914273-1952990	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv898594	chr12:1916838-1952990	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv898595	chr12:1916838-1962759	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv898596	chr12:1923040-1962759	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv898597	chr12:1928289-1962759	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1920000-1939400	Weak transcription	Gastric	stomach
2	chr12:1928400-1929800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:1928400-1933000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr12:1928400-1933200	Enhancers	Fetal Brain Male	brain
5	chr12:1928600-1930000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:1928600-1930800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
7	chr12:1928800-1929800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr12:1928800-1931400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr12:1929000-1929600	Active TSS	Brain Anterior Caudate	brain
10	chr12:1929000-1929800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
11	chr12:1929000-1929800	Enhancers	Spleen	Spleen
12	chr12:1929000-1930000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:1929000-1930200	Bivalent Enhancer	Fetal Thymus	thymus
14	chr12:1929000-1930800	Bivalent Enhancer	Placenta	Placenta
15	chr12:1929000-1931200	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:1929200-1929600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:1929200-1929600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:1929200-1929600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:1929200-1929600	Bivalent Enhancer	Right Ventricle	heart
20	chr12:1929200-1929800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr12:1929200-1929800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:1929200-1929800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:1929200-1929800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr12:1929200-1930000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
25	chr12:1929200-1930000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr12:1929200-1930000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr12:1929200-1930000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:1929200-1930000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr12:1929200-1930000	Bivalent Enhancer	Fetal Lung	lung
30	chr12:1929200-1930000	Bivalent Enhancer	HSMM	muscle
31	chr12:1929200-1930400	Bivalent Enhancer	Fetal Stomach	stomach
32	chr12:1929400-1929600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:1929400-1929600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
34	chr12:1929400-1929600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr12:1929400-1929800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr12:1929400-1929800	Active TSS	Brain Angular Gyrus	brain
37	chr12:1929400-1929800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
38	chr12:1929400-1930000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:1929400-1930000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:1929400-1930000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:1929400-1930000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:1929400-1931000	Bivalent Enhancer	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links