Variant report

Variant	rs12829711
Chromosome Location	chr12:4726297-4726298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4724909..4726859-chr12:4756521..4758491,2	K562	blood:
2	chr12:4717083..4718773-chr12:4723734..4726455,2	K562	blood:

Variant related genes	Relation type
ENSG00000111254	Chromatin interaction
ENSG00000139180	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11063280	0.81[ASN][1000 genomes]
rs11063282	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12303320	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12308883	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs12309713	0.85[CEU][hapmap]
rs12310639	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12313377	0.94[ASN][1000 genomes]
rs12318966	0.80[ASN][1000 genomes]
rs12811453	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12828416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16931616	0.84[CEU][hapmap];0.80[ASN][1000 genomes]
rs16931620	0.80[ASN][1000 genomes]
rs1860343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1990311	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs2072354	0.81[EUR][1000 genomes]
rs2267548	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs2299833	0.93[ASN][1000 genomes]
rs2302246	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs2884671	0.93[ASN][1000 genomes]
rs35131771	0.99[ASN][1000 genomes]
rs35167443	0.81[ASN][1000 genomes]
rs4147666	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4147667	0.86[CEU][hapmap]
rs4147671	0.81[ASN][1000 genomes]
rs4147672	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4147673	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs4147677	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs4147678	0.80[ASN][1000 genomes]
rs4147679	0.80[ASN][1000 genomes]
rs4147680	0.80[ASN][1000 genomes]
rs4147684	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs4147685	0.80[ASN][1000 genomes]
rs4766264	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4766267	0.94[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4766269	0.80[ASN][1000 genomes]
rs61909965	0.80[ASN][1000 genomes]
rs7136668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7312402	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7958182	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs7972657	0.80[ASN][1000 genomes]
rs7972737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7972920	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs7975484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7977981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs876586	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	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
4	nsv468986	chr12:4726068-4751798	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv557124	chr12:4726068-4751798	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12829711	AKAP3	cis	Esophagus Muscularis	GTEx
rs12829711	AKAP3	cis	Thyroid	GTEx
rs12829711	AKAP3	cis	Heart Left Ventricle	GTEx
rs12829711	AKAP3	cis	lung	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4714400-4726400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:4714600-4726800	Weak transcription	Right Ventricle	heart
3	chr12:4714800-4726600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:4715200-4726400	Weak transcription	Fetal Heart	heart
5	chr12:4716000-4726400	Weak transcription	HUVEC	blood vessel
6	chr12:4716000-4726400	Weak transcription	NHDF-Ad	bronchial
7	chr12:4716400-4726400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:4716400-4727200	Weak transcription	HepG2	liver
9	chr12:4720400-4726600	Weak transcription	NHEK	skin
10	chr12:4721200-4727200	Weak transcription	Psoas Muscle	Psoas
11	chr12:4723200-4726600	Weak transcription	Placenta	Placenta
12	chr12:4723200-4726600	Weak transcription	Small Intestine	intestine
13	chr12:4723400-4726800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:4723600-4726400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:4723600-4726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:4723600-4726800	Weak transcription	Fetal Stomach	stomach
17	chr12:4723600-4727000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:4723600-4727200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:4723600-4728200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:4723600-4735600	Weak transcription	HMEC	breast
21	chr12:4723800-4726800	Weak transcription	Thymus	Thymus
22	chr12:4723800-4727000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:4723800-4727400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:4723800-4728000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:4723800-4728600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:4723800-4732000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:4724000-4727000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:4724000-4727000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:4724000-4727200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:4724200-4726600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:4724200-4726800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:4724200-4726800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:4724200-4727400	Weak transcription	Fetal Thymus	thymus
34	chr12:4724200-4735600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:4724200-4756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:4724400-4726600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:4724400-4727200	Weak transcription	Osteobl	bone
38	chr12:4724400-4727600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:4724600-4726800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:4724800-4726400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:4724800-4727200	Weak transcription	Ovary	ovary
42	chr12:4724800-4727400	Weak transcription	HSMMtube	muscle
43	chr12:4724800-4729000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:4725000-4726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:4725000-4726800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:4725000-4727200	Weak transcription	Fetal Brain Female	brain
47	chr12:4725000-4727600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:4725200-4726800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:4725200-4726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:4725200-4726800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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