Variant report

Variant	rs58011896
Chromosome Location	chr18:12644680-12644681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12643324..12646056-chr18:12656295..12659962,4	MCF-7	breast:
2	chr18:12643422..12646156-chr18:12653146..12655533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11874912	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875203	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876168	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185471	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155734	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45460897	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55857671	1.00[ASN][1000 genomes]
rs55914043	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089701	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132337	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152190	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56271712	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56359953	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382499	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392324	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56792052	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56909423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61470666	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226376	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7243917	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244345	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870545	1.00[ASN][1000 genomes]
rs9646473	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12607800-12651800	Weak transcription	Brain Germinal Matrix	brain
2	chr18:12616400-12644800	Weak transcription	Brain Hippocampus Middle	brain
3	chr18:12616600-12645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12621200-12645200	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:12622800-12645000	Weak transcription	Brain Angular Gyrus	brain
6	chr18:12630400-12645400	Weak transcription	Ovary	ovary
7	chr18:12631000-12645200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:12631000-12645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr18:12631200-12647800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr18:12631400-12645200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
12	chr18:12635000-12645800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr18:12635200-12645800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12637800-12645400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr18:12637800-12652000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr18:12638800-12645000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr18:12638800-12645200	Weak transcription	Brain Anterior Caudate	brain
18	chr18:12639000-12644800	Weak transcription	Fetal Brain Female	brain
19	chr18:12639000-12645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr18:12639600-12645800	Weak transcription	Esophagus	oesophagus
21	chr18:12640400-12652000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr18:12640800-12645000	Weak transcription	Brain Substantia Nigra	brain
23	chr18:12641000-12644800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:12641000-12645200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr18:12641000-12645200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr18:12641000-12645200	Weak transcription	Pancreas	Pancrea
27	chr18:12641000-12645400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr18:12641000-12645400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:12641000-12645800	Weak transcription	K562	blood
30	chr18:12641000-12646000	Weak transcription	Right Ventricle	heart
31	chr18:12641000-12648200	Weak transcription	Hela-S3	cervix
32	chr18:12641200-12645200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr18:12641200-12645200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr18:12641200-12645200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr18:12641200-12645200	Weak transcription	Placenta	Placenta
36	chr18:12641200-12645400	Weak transcription	NH-A	brain
37	chr18:12641200-12645600	Weak transcription	Fetal Lung	lung
38	chr18:12641200-12645600	Weak transcription	NHDF-Ad	bronchial
39	chr18:12641200-12645800	Weak transcription	Lung	lung
40	chr18:12641400-12645000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:12641400-12647200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:12641600-12645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr18:12642200-12645600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:12642600-12645200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr18:12642600-12645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:12642600-12646200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr18:12642800-12644800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr18:12642800-12645400	Weak transcription	Left Ventricle	heart
49	chr18:12642800-12645600	Weak transcription	Adipose Nuclei	Adipose
50	chr18:12643200-12645600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links