Variant report

Variant	rs11063285
Chromosome Location	chr12:4763069-4763070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:4757063..4759938-chr12:4760465..4764038,5	K562	blood:
2	chr12:4754845..4760714-chr12:4761830..4765057,7	MCF-7	breast:
3	chr12:4756861..4759668-chr12:4760395..4765208,7	MCF-7	breast:
4	chr12:4757573..4759938-chr12:4760465..4764276,3	K562	blood:
5	chr12:4762857..4765662-chr12:4767685..4769794,2	K562	blood:
6	chr12:4762342..4764303-chr12:4764418..4767058,2	K562	blood:

Variant related genes	Relation type
ENSG00000139180	Chromatin interaction
ENSG00000111254	Chromatin interaction
ENSG00000255639	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11063280	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063282	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614014	0.84[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs11614030	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs12303320	0.82[ASN][1000 genomes]
rs12308883	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12309713	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12310639	0.86[ASN][1000 genomes]
rs12313377	0.84[ASN][1000 genomes]
rs12318966	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12811453	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16931616	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16931620	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1860343	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs1990311	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267548	0.92[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299833	0.83[ASN][1000 genomes]
rs2302246	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884671	0.81[ASN][1000 genomes]
rs35167443	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147667	0.83[EUR][1000 genomes]
rs4147671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147672	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147673	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147677	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147678	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147679	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147680	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147682	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4147684	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147685	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4766264	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs4766267	0.92[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs4766269	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61909965	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7136668	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs7312402	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7958182	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972657	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972737	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs7972920	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7977981	0.84[CHB][hapmap]
rs876586	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv898617	chr12:4715082-4768619	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898618	chr12:4726068-4764137	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898619	chr12:4737715-4771456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv898620	chr12:4745313-4771456	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv557125	chr12:4748410-4764137	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036308	chr12:4748657-4804156	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv898621	chr12:4751798-4768193	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv898622	chr12:4751798-4768619	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv898623	chr12:4751798-4771456	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv898624	chr12:4757474-4769876	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv557126	chr12:4757809-4768619	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv898625	chr12:4759380-4771682	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11063285	AKAP3	cis	Thyroid	GTEx
rs11063285	AKAP3	cis	lung	GTEx
rs11063285	AKAP3	cis	Muscle Skeletal	GTEx
rs11063285	DYRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4758800-4763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:4759000-4763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:4759000-4763400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:4759000-4763400	Weak transcription	Spleen	Spleen
5	chr12:4759000-4764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:4759000-4764000	Weak transcription	Lung	lung
7	chr12:4759000-4764200	Weak transcription	Esophagus	oesophagus
8	chr12:4759000-4764400	Weak transcription	Aorta	Aorta
9	chr12:4759000-4764400	Weak transcription	Pancreas	Pancrea
10	chr12:4759000-4772600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:4759200-4763400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:4759200-4763400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:4759200-4763400	Weak transcription	Ovary	ovary
15	chr12:4759200-4763400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:4759200-4764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:4759200-4764400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:4759200-4776200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:4759400-4763400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:4759400-4763400	Weak transcription	HSMMtube	muscle
21	chr12:4759400-4764800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:4759400-4767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:4759600-4763400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:4759600-4763400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:4759600-4763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:4759600-4763400	Weak transcription	Left Ventricle	heart
27	chr12:4759600-4763400	Weak transcription	NH-A	brain
28	chr12:4759600-4764400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:4759600-4764800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:4759600-4767000	Weak transcription	Stomach Mucosa	stomach
31	chr12:4759800-4763200	Weak transcription	HSMM	muscle
32	chr12:4759800-4763400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:4759800-4763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:4759800-4763400	Weak transcription	Fetal Kidney	kidney
35	chr12:4759800-4763400	Weak transcription	Fetal Stomach	stomach
36	chr12:4759800-4763400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:4759800-4763600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:4759800-4763600	Weak transcription	Colonic Mucosa	Colon
39	chr12:4759800-4764200	Weak transcription	NHLF	lung
40	chr12:4760000-4763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:4760000-4763200	Weak transcription	Osteobl	bone
42	chr12:4760000-4763400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:4760000-4763400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:4760000-4763400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:4760000-4763400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:4760000-4763400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:4760000-4763400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:4760000-4763400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:4760000-4763400	Weak transcription	Brain Angular Gyrus	brain
50	chr12:4760000-4763400	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links