Variant report

Variant	rs12828259
Chromosome Location	chr12:65050948-65050949
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:65047034..65048625-chr12:65050187..65053133,2	K562	blood:
2	chr12:64989952..64991972-chr12:65050682..65053342,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12812333	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12815802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820666	0.89[EUR][1000 genomes]
rs35011112	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35127263	0.89[EUR][1000 genomes]
rs35846274	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964087	0.85[ASN][1000 genomes]
rs55668439	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56136505	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56206108	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61931658	0.84[EUR][1000 genomes]
rs67264294	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9788201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription 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 miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
2	chr12:65028600-65056400	Weak transcription	NHEK	skin
3	chr12:65033000-65052600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:65033600-65059400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:65038200-65051200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:65041600-65052200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:65043600-65059600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:65044000-65059400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:65044200-65051400	Weak transcription	Colonic Mucosa	Colon
10	chr12:65044600-65051000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:65045000-65051000	Weak transcription	GM12878-XiMat	blood
12	chr12:65045600-65054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:65045800-65051000	Weak transcription	Gastric	stomach
14	chr12:65045800-65056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:65046400-65058600	Weak transcription	Ovary	ovary
16	chr12:65046600-65051800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:65047000-65051400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:65047000-65056400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:65047000-65059400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:65047200-65051200	Weak transcription	Spleen	Spleen
21	chr12:65047200-65059400	Weak transcription	Fetal Stomach	stomach
22	chr12:65047400-65059400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:65047800-65051200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:65047800-65051600	Weak transcription	Aorta	Aorta
25	chr12:65047800-65051600	Weak transcription	Right Ventricle	heart
26	chr12:65047800-65051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:65047800-65052600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:65047800-65056000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:65047800-65056400	Weak transcription	Hela-S3	cervix
30	chr12:65047800-65056600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:65047800-65059400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:65047800-65059400	Weak transcription	NHLF	lung
33	chr12:65047800-65063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:65048000-65051200	Weak transcription	HMEC	breast
35	chr12:65048000-65052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:65048000-65060400	Weak transcription	Dnd41	blood
37	chr12:65048000-65063000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:65048400-65051200	Weak transcription	Left Ventricle	heart
39	chr12:65048400-65062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:65048600-65053400	Enhancers	HepG2	liver
41	chr12:65048600-65054600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:65048600-65059400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:65048800-65051800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:65048800-65051800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr12:65048800-65060200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr12:65049000-65051400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:65049000-65052000	Weak transcription	Adipose Nuclei	Adipose
48	chr12:65049000-65059600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:65049200-65052600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:65049200-65053600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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