Variant report

Variant	rs2267548
Chromosome Location	chr12:4771456-4771457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11063280	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063282	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063285	0.92[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11614014	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11614030	0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12303320	0.84[ASN][1000 genomes]
rs12308883	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12309713	0.90[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12310639	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12313377	0.84[ASN][1000 genomes]
rs12318966	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811453	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828416	0.81[ASN][1000 genomes]
rs12829711	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs16931616	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16931620	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1860343	0.83[ASN][1000 genomes]
rs1990311	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072354	0.81[EUR][1000 genomes]
rs2299833	0.83[ASN][1000 genomes]
rs2302246	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35131771	0.81[ASN][1000 genomes]
rs35167443	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147666	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4147667	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4147671	0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147672	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147673	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147677	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147678	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147679	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147680	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147682	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147684	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147685	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4766264	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4766267	0.89[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4766269	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61909965	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136668	0.83[ASN][1000 genomes]
rs7312402	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958182	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972657	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972737	0.83[ASN][1000 genomes]
rs7972920	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975484	0.81[ASN][1000 genomes]
rs7977981	0.81[ASN][1000 genomes]
rs876586	0.83[EUR][1000 genomes];0.88[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	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	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
3	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
4	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
5	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
6	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
7	esv3362685	chr12:4770868-4776681	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2267548	AKAP3	cis	Thyroid	GTEx
rs2267548	AKAP3	cis	Esophagus Muscularis	GTEx
rs2267548	AKAP3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4759000-4772600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:4759200-4776200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:4760800-4782400	Strong transcription	Primary T cells from cord blood	blood
5	chr12:4761800-4782200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:4762200-4779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:4762200-4783600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:4762600-4773000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:4762600-4773400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:4762600-4779600	Strong transcription	Primary hematopoietic stem cells	blood
11	chr12:4762600-4780000	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:4762600-4782800	Strong transcription	Adipose Nuclei	Adipose
13	chr12:4762800-4779800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:4762800-4781000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:4762800-4782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:4763000-4774800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:4763000-4775600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:4763000-4780400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:4763000-4782200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:4763000-4782400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:4763000-4782400	Strong transcription	Placenta	Placenta
22	chr12:4763000-4783000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr12:4763200-4772600	Strong transcription	HSMM	muscle
24	chr12:4763200-4772600	Strong transcription	Osteobl	bone
25	chr12:4763200-4773600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:4763200-4782200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:4763400-4771600	Strong transcription	Ovary	ovary
28	chr12:4763400-4771600	Strong transcription	Thymus	Thymus
29	chr12:4763400-4771800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:4763400-4771800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:4763400-4772400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:4763400-4772600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:4763400-4772600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:4763400-4772600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:4763400-4772600	Strong transcription	HSMMtube	muscle
36	chr12:4763400-4773200	Strong transcription	Right Ventricle	heart
37	chr12:4763400-4773600	Strong transcription	HMEC	breast
38	chr12:4763400-4774000	Strong transcription	HUVEC	blood vessel
39	chr12:4763400-4774200	Strong transcription	Rectal Smooth Muscle	rectum
40	chr12:4763400-4774600	Strong transcription	HepG2	liver
41	chr12:4763400-4774800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:4763400-4774800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:4763400-4774800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:4763400-4774800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:4763400-4775200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:4763400-4775200	Strong transcription	A549	lung
47	chr12:4763400-4775400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:4763400-4775600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:4763400-4779200	Strong transcription	Brain Germinal Matrix	brain
50	chr12:4763400-4779600	Strong transcription	Fetal Muscle Trunk	muscle

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