Variant report

Variant	rs11614030
Chromosome Location	chr12:4769876-4769877
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11063280	0.84[EUR][1000 genomes]
rs11063282	1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs11063285	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs11614014	0.85[CEU][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12308883	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12309713	0.81[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12318966	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12811453	1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16931616	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16931620	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1990311	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2267548	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]
rs2302246	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs35167443	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4147666	0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4147667	0.81[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs4147671	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs4147672	1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4147673	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4147677	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4147678	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4147679	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4147680	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4147682	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4147684	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4147685	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4766264	0.94[MEX][hapmap];0.88[TSI][hapmap]
rs4766267	0.88[JPT][hapmap]
rs4766269	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61909965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7312402	0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs7958182	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7972657	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7972920	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][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	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
7	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11614030	AKAP3	cis	parietal	SCAN
rs11614030	ADIPOR2	cis	parietal	SCAN
rs11614030	GPR162	cis	parietal	SCAN
rs11614030	GNB3	cis	cerebellum	SCAN
rs11614030	CACNA1C	cis	cerebellum	SCAN
rs11614030	AKAP3	cis	Esophagus Muscularis	GTEx
rs11614030	NDUFA9	cis	parietal	SCAN
rs11614030	AKAP3	cis	Thyroid	GTEx
rs11614030	RAD52	cis	parietal	SCAN
rs11614030	ACRBP	cis	parietal	SCAN
rs11614030	CLSTN3	cis	cerebellum	SCAN
rs11614030	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs11614030	AKAP3	cis	lung	GTEx
rs11614030	AKAP3	cis	cerebellum	SCAN

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	chr12:4763400-4771200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:4763400-4771200	Strong transcription	Fetal Stomach	stomach
29	chr12:4763400-4771400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:4763400-4771400	Strong transcription	Spleen	Spleen
31	chr12:4763400-4771400	Strong transcription	NHEK	skin
32	chr12:4763400-4771600	Strong transcription	Ovary	ovary
33	chr12:4763400-4771600	Strong transcription	Thymus	Thymus
34	chr12:4763400-4771800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:4763400-4771800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:4763400-4772400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:4763400-4772600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:4763400-4772600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:4763400-4772600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:4763400-4772600	Strong transcription	HSMMtube	muscle
41	chr12:4763400-4773200	Strong transcription	Right Ventricle	heart
42	chr12:4763400-4773600	Strong transcription	HMEC	breast
43	chr12:4763400-4774000	Strong transcription	HUVEC	blood vessel
44	chr12:4763400-4774200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr12:4763400-4774600	Strong transcription	HepG2	liver
46	chr12:4763400-4774800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:4763400-4774800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:4763400-4774800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:4763400-4774800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:4763400-4775200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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