Variant report

Variant	rs542666842
Chromosome Location	chr12:40500548-40500549
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	ZNF263	chr12:40499084-40500634	HEK293-T-REx	kidney:	n/a	n/a
2	STAT3	chr12:40500378-40500726	MCF10A-Er-Src	breast:	n/a	chr12:40500548-40500568 chr12:40500554-40500562 chr12:40500552-40500563 chr12:40500551-40500565
3	STAT3	chr12:40500366-40500744	MCF10A-Er-Src	breast:	n/a	chr12:40500548-40500568 chr12:40500554-40500562 chr12:40500552-40500563 chr12:40500551-40500565
4	STAT3	chr12:40500369-40500754	MCF10A-Er-Src	breast:	n/a	chr12:40500548-40500568 chr12:40500554-40500562 chr12:40500552-40500563 chr12:40500551-40500565
5	STAT3	chr12:40500366-40500843	MCF10A-Er-Src	breast:	n/a	chr12:40500548-40500568 chr12:40500554-40500562 chr12:40500552-40500563 chr12:40500551-40500565
6	KAP1	chr12:40500195-40501769	HEK293	kidney:	n/a	n/a
7	MXI1	chr12:40498470-40500612	SK-N-SH	brain:	n/a	n/a
8	E2F4	chr12:40499753-40500744	MCF10A-Er-Src	breast:	n/a	chr12:40499879-40499890 chr12:40499878-40499890 chr12:40499961-40499971

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40404217..40405558-chr12:40500388..40503110,15	MCF-7	breast:
2	chr12:40413403..40416172-chr12:40500145..40501731,2	K562	blood:

Variant related genes	Relation type
SLC2A13	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	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
6	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
7	esv3436452	chr12:40498510-40501058	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
8	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 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	chr12:40496800-40501600	Active TSS	Brain Cingulate Gyrus	brain
2	chr12:40496800-40501600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:40496800-40501600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:40497000-40501600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr12:40497000-40501600	Active TSS	Fetal Kidney	kidney
6	chr12:40497200-40502200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:40497400-40501600	Active TSS	Right Atrium	heart
8	chr12:40497800-40500600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr12:40497800-40501400	Active TSS	Brain Substantia Nigra	brain
10	chr12:40497800-40501400	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr12:40498000-40500800	Active TSS	Rectal Smooth Muscle	rectum
12	chr12:40498000-40501600	Active TSS	Ovary	ovary
13	chr12:40498200-40501800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr12:40498200-40501800	Active TSS	NHLF	lung
15	chr12:40498400-40501600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:40498600-40501600	Active TSS	Aorta	Aorta
17	chr12:40498800-40501000	Active TSS	Pancreas	Pancrea
18	chr12:40498800-40501600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:40498800-40501600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:40499000-40500600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:40499000-40501400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr12:40499000-40501400	Active TSS	Colonic Mucosa	Colon
23	chr12:40499000-40501400	Active TSS	Esophagus	oesophagus
24	chr12:40499000-40501400	Active TSS	Left Ventricle	heart
25	chr12:40499000-40501600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:40499000-40501600	Active TSS	Brain Anterior Caudate	brain
27	chr12:40499000-40501600	Active TSS	Duodenum Mucosa	Duodenum
28	chr12:40499200-40500800	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:40499200-40501400	Active TSS	Fetal Muscle Leg	muscle
30	chr12:40499200-40501600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:40499200-40501600	Active TSS	NH-A	brain
32	chr12:40499800-40501600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:40499800-40501600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:40499800-40501600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:40500000-40500600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:40500000-40500600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:40500000-40500600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:40500000-40500600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
39	chr12:40500000-40500800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:40500000-40501000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:40500000-40501200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:40500000-40501200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr12:40500000-40501200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:40500000-40501400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr12:40500000-40501400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr12:40500000-40501400	Flanking Active TSS	Hela-S3	cervix
47	chr12:40500000-40501400	Flanking Active TSS	HMEC	breast
48	chr12:40500000-40501600	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr12:40500200-40500600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:40500200-40500600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links