Variant report

Variant	rs12820559
Chromosome Location	chr12:51565619-51565620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51564751..51566966-chr12:51783543..51785825,2	K562	blood:
2	chr12:51474365..51478814-chr12:51563597..51568148,9	K562	blood:
3	chr12:51564447..51569582-chr12:51630930..51635335,8	K562	blood:
4	chr12:51557800..51560128-chr12:51563372..51565944,2	K562	blood:
5	chr12:51563450..51568971-chr12:51609008..51613972,14	K562	blood:
6	chr12:51565300..51568760-chr12:51661642..51664290,3	K562	blood:
7	chr12:51565491..51567919-chr12:51611128..51615638,5	K562	blood:
8	chr12:51474365..51480004-chr12:51564069..51568503,12	K562	blood:
9	chr12:51564257..51569582-chr12:51630930..51636873,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184271	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000050438	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1056897	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169726	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169727	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169729	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169731	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169732	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169742	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11169743	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11169752	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169754	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11738	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11831810	0.80[JPT][hapmap]
rs11833022	0.81[JPT][hapmap]
rs11834746	0.81[JPT][hapmap]
rs12809832	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12810455	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12810596	0.84[AMR][1000 genomes]
rs12810700	1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs12811508	0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12811684	0.81[JPT][hapmap]
rs12813368	0.82[AMR][1000 genomes]
rs12814498	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12815367	0.87[ASN][1000 genomes]
rs12819225	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12819517	0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12820966	0.82[AMR][1000 genomes]
rs12823402	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12826153	0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs12829630	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12833565	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17296192	0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34057357	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34481246	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34498074	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580784	0.81[JPT][hapmap]
rs6580792	0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580793	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67293043	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7954140	0.81[JPT][hapmap]
rs7955251	0.87[ASN][1000 genomes]
rs7958064	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7960381	0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7964570	0.88[AMR][1000 genomes]
rs7976777	0.84[AMR][1000 genomes]
rs7977104	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs970098	0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
2	chr12:51564200-51565800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:51564200-51566200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:51564600-51566000	Flanking Active TSS	Dnd41	blood
5	chr12:51564800-51565800	Flanking Active TSS	Hela-S3	cervix
6	chr12:51564800-51566000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51564800-51566200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr12:51564800-51567200	Active TSS	HSMMtube	muscle
9	chr12:51564800-51567400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:51564800-51567400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:51564800-51567400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:51564800-51567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:51564800-51567400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:51564800-51567400	Active TSS	HMEC	breast
15	chr12:51565000-51565800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:51565000-51565800	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:51565000-51565800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:51565000-51565800	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr12:51565000-51565800	Flanking Active TSS	HUVEC	blood vessel
20	chr12:51565000-51565800	Flanking Active TSS	NHEK	skin
21	chr12:51565000-51565800	Flanking Active TSS	Osteobl	bone
22	chr12:51565000-51566000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:51565000-51566000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr12:51565000-51566200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:51565000-51567000	Active TSS	NH-A	brain
26	chr12:51565000-51567400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr12:51565000-51567400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:51565000-51567400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:51565000-51567400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:51565000-51567400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr12:51565000-51567400	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:51565000-51567400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:51565000-51567400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr12:51565000-51567400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:51565000-51567400	Active TSS	NHLF	lung
36	chr12:51565000-51567800	Active TSS	K562	blood
37	chr12:51565200-51565800	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr12:51565200-51566000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr12:51565200-51566000	Enhancers	Spleen	Spleen
40	chr12:51565200-51566200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:51565200-51566200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:51565200-51566600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr12:51565200-51567200	Active TSS	NHDF-Ad	bronchial
44	chr12:51565200-51567400	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr12:51565200-51567400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:51565200-51567400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:51565200-51567400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr12:51565200-51567400	Active TSS	GM12878-XiMat	blood
49	chr12:51565200-51567400	Active TSS	HSMM	muscle
50	chr12:51565200-51568600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links