Variant report

Variant	rs2062528
Chromosome Location	chr12:117480224-117480225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117477087..117480724-chr12:117486826..117489814,3	MCF-7	breast:
2	chr12:117470652..117475607-chr12:117477009..117480553,6	K562	blood:
3	chr12:117478356..117481644-chr12:117536617..117538572,3	K562	blood:
4	chr12:117478764..117480337-chr12:117507542..117509492,2	K562	blood:
5	chr12:117478574..117480262-chr12:117481796..117483489,2	K562	blood:
6	chr12:117474107..117476260-chr12:117479053..117480965,2	K562	blood:

Variant related genes	Relation type
ENSG00000088992	Chromatin interaction
ENSG00000258285	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735100	0.95[JPT][hapmap]
rs10735101	0.95[JPT][hapmap]
rs10744887	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774895	0.94[JPT][hapmap]
rs10774898	0.94[JPT][hapmap]
rs10774899	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850734	0.95[JPT][hapmap]
rs10850745	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850746	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850747	0.96[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10850751	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10850752	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11068299	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068300	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11068301	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068306	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611741	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11832441	0.89[EUR][1000 genomes]
rs11834817	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11837022	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12368876	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1472523	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173654	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291911	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs2291916	0.94[JPT][hapmap]
rs2393124	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782191	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782192	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs4766816	0.95[JPT][hapmap]
rs4766823	0.94[JPT][hapmap]
rs4766825	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767477	0.94[JPT][hapmap]
rs55969361	0.89[EUR][1000 genomes]
rs58470318	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59756806	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6490103	0.94[JPT][hapmap]
rs6490104	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490105	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6490106	0.92[CEU][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6490107	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7133090	0.94[JPT][hapmap]
rs7294692	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297303	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297917	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486428	0.94[JPT][hapmap]
rs7953553	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956481	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960638	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960731	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964668	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964686	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs7968761	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7968891	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971795	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972416	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7978810	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs9634171	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:117471600-117482600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:117472000-117482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:117476400-117484600	Weak transcription	Dnd41	blood
8	chr12:117477400-117481200	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:117477400-117481400	Enhancers	Stomach Mucosa	stomach
10	chr12:117477400-117482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:117477400-117482800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:117477400-117483000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:117477400-117484800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:117477600-117482800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:117477800-117482800	Weak transcription	Fetal Brain Female	brain
16	chr12:117478000-117482800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:117478200-117482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:117478200-117482800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:117478200-117482800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:117478400-117481600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:117478400-117482800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:117478600-117480400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr12:117478800-117480400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr12:117478800-117482400	Weak transcription	Fetal Thymus	thymus
25	chr12:117479600-117480600	Enhancers	Spleen	Spleen
26	chr12:117479600-117480800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:117479600-117481200	Enhancers	Fetal Intestine Large	intestine
28	chr12:117479600-117481200	Enhancers	Fetal Intestine Small	intestine
29	chr12:117479600-117481600	Enhancers	Left Ventricle	heart
30	chr12:117479600-117488000	Enhancers	Fetal Heart	heart
31	chr12:117479800-117480400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:117479800-117480400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:117479800-117480400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:117479800-117480400	Genic enhancers	Right Atrium	heart
35	chr12:117479800-117480400	Enhancers	Right Ventricle	heart
36	chr12:117479800-117480600	Enhancers	Placenta	Placenta
37	chr12:117479800-117480800	Enhancers	Gastric	stomach
38	chr12:117479800-117481200	Enhancers	Hela-S3	cervix
39	chr12:117479800-117481200	Flanking Active TSS	K562	blood
40	chr12:117479800-117481400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:117480000-117480600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:117480000-117480600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:117480000-117480600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:117480000-117480600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:117480000-117480600	Genic enhancers	Pancreas	Pancrea
46	chr12:117480000-117480600	Genic enhancers	HepG2	liver
47	chr12:117480000-117481200	Enhancers	A549	lung
48	chr12:117480200-117480600	Enhancers	Esophagus	oesophagus
49	chr12:117480200-117480600	Enhancers	Ovary	ovary
50	chr12:117480200-117480800	Enhancers	HSMMtube	muscle

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