Variant report

Variant	rs552409998
Chromosome Location	chr12:40498488-40498489
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39835235..39837376-chr12:40497652..40499874,2	K562	blood:
2	chr12:40494859..40496427-chr12:40496570..40499467,2	MCF-7	breast:
3	chr11:62607295..62609623-chr12:40497021..40499693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1816874	chr12:40492814-40499934	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	esv1822895	chr12:40492814-40499934	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
6	esv1838004	chr12:40492814-40499934	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
7	esv1841992	chr12:40492814-40499934	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	esv1850635	chr12:40492814-40499934	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
9	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1839896	chr12:40493591-40499908	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
12	esv1834762	chr12:40496733-40499934	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
13	esv1799112	chr12:40497095-40499908	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
14	esv1840625	chr12:40497095-40499908	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
15	esv3359383	chr12:40498110-40500658	Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
16	esv1841522	chr12:40498190-40499803	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
17	esv1822852	chr12:40498190-40499934	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
18	esv1844742	chr12:40498190-40499934	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
19	esv1847923	chr12:40498190-40499934	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
20	esv1835713	chr12:40498326-40499803	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
21	esv1836654	chr12:40498326-40499908	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
22	esv1839194	chr12:40498326-40499908	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
23	esv1845368	chr12:40498326-40499908	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40488200-40498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:40492400-40498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:40492800-40498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:40492800-40498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:40492800-40498600	Weak transcription	Lung	lung
6	chr12:40496800-40498600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:40496800-40498600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:40496800-40499000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr12:40496800-40500400	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:40496800-40501600	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:40496800-40501600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:40496800-40501600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:40497000-40498600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:40497000-40498600	Enhancers	Liver	Liver
15	chr12:40497000-40498600	Weak transcription	Psoas Muscle	Psoas
16	chr12:40497000-40498600	Active TSS	Right Ventricle	heart
17	chr12:40497000-40498800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:40497000-40498800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:40497000-40498800	Flanking Active TSS	Hela-S3	cervix
20	chr12:40497000-40499000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:40497000-40500200	Active TSS	Brain Angular Gyrus	brain
22	chr12:40497000-40501600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:40497000-40501600	Active TSS	Fetal Kidney	kidney
24	chr12:40497200-40498600	Weak transcription	Pancreas	Pancrea
25	chr12:40497200-40498800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:40497200-40499000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:40497200-40502200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:40497400-40498600	Active TSS	Brain Anterior Caudate	brain
29	chr12:40497400-40498800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:40497400-40498800	Enhancers	Fetal Heart	heart
31	chr12:40497400-40499000	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr12:40497400-40500000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:40497400-40501600	Active TSS	Right Atrium	heart
34	chr12:40497600-40498600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr12:40497600-40499000	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr12:40497600-40500400	Active TSS	Fetal Brain Female	brain
37	chr12:40497800-40498600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr12:40497800-40498600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:40497800-40498600	Weak transcription	Fetal Brain Male	brain
40	chr12:40497800-40498600	Enhancers	Placenta	Placenta
41	chr12:40497800-40498600	Bivalent/Poised TSS	GM12878-XiMat	blood
42	chr12:40497800-40498800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:40497800-40498800	Flanking Active TSS	HepG2	liver
44	chr12:40497800-40499000	Enhancers	Spleen	Spleen
45	chr12:40497800-40499200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:40497800-40500200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:40497800-40500400	Active TSS	Brain Hippocampus Middle	brain
48	chr12:40497800-40500600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr12:40497800-40501400	Active TSS	Brain Substantia Nigra	brain
50	chr12:40497800-40501400	Active TSS	Sigmoid Colon	Sigmoid Colon

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