Variant report

Variant	rs758532
Chromosome Location	chr12:4714557-4714558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:4713666-4715111	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr12:4713543-4714587	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr12:4713654-4714793	IMR90	lung:	n/a	n/a
4	PML	chr12:4713730-4714581	GM12878	blood:	n/a	chr12:4714055-4714063
5	HCFC1	chr12:4713602-4714699	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr12:4713545-4714711	A549	lung:	n/a	chr12:4713977-4713990

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4712076..4715630-chr12:4717272..4720188,3	K562	blood:

Variant related genes	Relation type
ENSG00000256748	TF binding region
DYRK4	TF binding region
ENSG00000010219	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10444481	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774249	0.82[CEU][hapmap]
rs10774252	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774253	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774254	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849109	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849110	0.92[ASN][1000 genomes]
rs11063261	0.87[CEU][hapmap]
rs11063267	0.85[ASN][1000 genomes]
rs11063270	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227238	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12298137	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12366671	0.87[CEU][hapmap]
rs1860342	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2011298	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072355	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs2072356	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs2267544	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267547	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299834	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147675	0.83[CEU][hapmap];0.87[CHB][hapmap]
rs6416316	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs7133467	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7133999	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7300882	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7301072	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310920	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310971	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7311845	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917565	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917566	0.92[EUR][1000 genomes]
rs997373	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs758532	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs758532	AKAP3	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4713600-4714600	Active TSS	Brain Anterior Caudate	brain
2	chr12:4713600-4714800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:4713600-4714800	Active TSS	Fetal Kidney	kidney
4	chr12:4713600-4715000	Active TSS	HSMM	muscle
5	chr12:4713800-4714600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr12:4713800-4714600	Active TSS	Primary monocytes fromperipheralblood	blood
7	chr12:4713800-4714600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr12:4713800-4714600	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr12:4713800-4714600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr12:4713800-4714600	Active TSS	Aorta	Aorta
11	chr12:4713800-4714600	Active TSS	Brain Germinal Matrix	brain
12	chr12:4713800-4714600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr12:4713800-4714600	Active TSS	Fetal Brain Female	brain
14	chr12:4713800-4714600	Active TSS	Thymus	Thymus
15	chr12:4713800-4714600	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr12:4713800-4714800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:4713800-4714800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:4713800-4714800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:4713800-4714800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:4713800-4714800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:4713800-4714800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:4713800-4714800	Active TSS	Brain Substantia Nigra	brain
23	chr12:4713800-4714800	Active TSS	Fetal Lung	lung
24	chr12:4713800-4714800	Active TSS	Fetal Thymus	thymus
25	chr12:4713800-4714800	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:4713800-4714800	Active TSS	HSMMtube	muscle
27	chr12:4713800-4715000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:4713800-4715000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr12:4713800-4715000	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:4713800-4715000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:4713800-4715000	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr12:4713800-4715000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:4713800-4715000	Active TSS	Muscle Satellite Cultured Cells	--
34	chr12:4713800-4715000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:4713800-4715000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:4713800-4715000	Active TSS	Brain Angular Gyrus	brain
37	chr12:4713800-4715000	Active TSS	Brain Hippocampus Middle	brain
38	chr12:4713800-4715000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:4713800-4715000	Active TSS	Colon Smooth Muscle	Colon
40	chr12:4713800-4715000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr12:4713800-4715000	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:4713800-4715000	Active TSS	A549	lung
43	chr12:4713800-4715000	Active TSS	Hela-S3	cervix
44	chr12:4713800-4715000	Active TSS	NH-A	brain
45	chr12:4713800-4715000	Active TSS	NHDF-Ad	bronchial
46	chr12:4713800-4715000	Active TSS	NHEK	skin
47	chr12:4713800-4715000	Active TSS	Osteobl	bone
48	chr12:4713800-4715200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr12:4713800-4715200	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:4713800-4715200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links