Variant report

Variant	rs11172820
Chromosome Location	chr12:59308003-59308004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59270433..59273338-chr12:59306746..59309338,2	MCF-7	breast:
2	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:
3	chr12:59305986..59308290-chr12:59311470..59314122,2	K562	blood:

Variant related genes	Relation type
ENSG00000257443	Chromatin interaction
ENSG00000139263	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10783927	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291799	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291800	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
2	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:59290600-59311000	Weak transcription	Right Ventricle	heart
5	chr12:59292400-59309200	Weak transcription	Fetal Heart	heart
6	chr12:59292400-59310600	Weak transcription	Small Intestine	intestine
7	chr12:59301200-59309400	Weak transcription	GM12878-XiMat	blood
8	chr12:59302000-59313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:59302200-59309200	Weak transcription	Ovary	ovary
10	chr12:59302400-59308200	Weak transcription	Aorta	Aorta
11	chr12:59302400-59309000	Weak transcription	A549	lung
12	chr12:59302800-59309400	Weak transcription	Pancreas	Pancrea
13	chr12:59302800-59309600	Weak transcription	Colonic Mucosa	Colon
14	chr12:59303200-59313400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:59303800-59308200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:59303800-59309400	Weak transcription	Esophagus	oesophagus
17	chr12:59303800-59311800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:59303800-59312400	Weak transcription	Gastric	stomach
19	chr12:59303800-59313000	Weak transcription	Lung	lung
20	chr12:59304000-59308200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:59304800-59312800	Weak transcription	Placenta	Placenta
22	chr12:59305000-59308800	Weak transcription	Brain Anterior Caudate	brain
23	chr12:59305000-59309200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:59305000-59309400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:59305200-59308200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:59305200-59308400	Weak transcription	Brain Substantia Nigra	brain
27	chr12:59305200-59309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:59305200-59309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:59305200-59309400	Weak transcription	Psoas Muscle	Psoas
30	chr12:59305200-59309600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:59305200-59310600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:59305800-59308800	Enhancers	Stomach Mucosa	stomach
33	chr12:59306200-59308200	Strong transcription	NHEK	skin
34	chr12:59306400-59308200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:59306400-59308600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:59306600-59313000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:59306800-59309000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr12:59306800-59309400	Enhancers	HepG2	liver
39	chr12:59306800-59310400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:59307000-59308200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr12:59307400-59308200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:59307400-59308400	Active TSS	Fetal Brain Female	brain
43	chr12:59307400-59308800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:59307400-59309200	Enhancers	Fetal Intestine Small	intestine
45	chr12:59307400-59310800	Weak transcription	Hela-S3	cervix
46	chr12:59307600-59308200	Weak transcription	Liver	Liver
47	chr12:59307600-59308200	Weak transcription	Osteobl	bone
48	chr12:59307600-59308600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:59307600-59308600	Enhancers	Fetal Brain Male	brain
50	chr12:59307600-59308600	Weak transcription	Rectal Mucosa Donor 29	rectum

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