Variant report

Variant	rs12623239
Chromosome Location	chr2:178158043-178158044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178157367..178160331-chr2:178462201..178464418,2	K562	blood:
2	chr2:178127910..178130801-chr2:178157421..178159180,2	MCF-7	breast:
3	chr2:178127315..178131627-chr2:178155428..178160936,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000222043	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10179735	0.94[CEU][hapmap]
rs10179975	0.94[CEU][hapmap]
rs10207932	0.94[CEU][hapmap]
rs10497510	0.81[EUR][1000 genomes]
rs10930784	0.94[CEU][hapmap]
rs10930785	0.94[CEU][hapmap]
rs12987686	0.94[CEU][hapmap]
rs12992747	0.82[EUR][1000 genomes]
rs13001890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002088	1.00[CEU][hapmap];0.82[CHD][hapmap];0.86[EUR][1000 genomes]
rs13017003	1.00[JPT][hapmap]
rs13410559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1377491	1.00[CEU][hapmap]
rs1453376	1.00[CEU][hapmap]
rs1463287	0.82[EUR][1000 genomes]
rs1463288	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1466208	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1551287	0.82[EUR][1000 genomes]
rs1551288	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1551289	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1551290	0.82[EUR][1000 genomes]
rs1597958	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597959	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17648502	0.82[EUR][1000 genomes]
rs1869358	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1901828	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1973044	0.82[EUR][1000 genomes]
rs1973045	0.82[EUR][1000 genomes]
rs1973047	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123644	0.82[EUR][1000 genomes]
rs2123645	0.82[EUR][1000 genomes]
rs2167904	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2364733	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2364847	0.94[CEU][hapmap]
rs2364848	0.94[CEU][hapmap];0.84[MEX][hapmap]
rs2444563	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2444564	0.82[EUR][1000 genomes]
rs2464655	0.82[EUR][1000 genomes]
rs2602527	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2602528	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706143	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706144	0.82[EUR][1000 genomes]
rs2706145	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706146	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706147	1.00[CEU][hapmap]
rs2706150	0.82[EUR][1000 genomes]
rs2706153	0.82[EUR][1000 genomes]
rs2706154	0.82[EUR][1000 genomes]
rs2706155	0.82[EUR][1000 genomes]
rs2706156	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706157	0.82[EUR][1000 genomes]
rs2706158	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706162	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2706163	0.82[EUR][1000 genomes]
rs2886194	1.00[JPT][hapmap]
rs4130304	0.94[CEU][hapmap]
rs4893930	0.94[CEU][hapmap]
rs56951837	0.82[EUR][1000 genomes]
rs6414095	1.00[CEU][hapmap];0.82[CHD][hapmap]
rs6731409	0.82[EUR][1000 genomes]
rs6732256	1.00[CEU][hapmap]
rs72946169	0.82[EUR][1000 genomes]
rs7559715	1.00[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7566603	0.82[EUR][1000 genomes]
rs7566686	0.82[EUR][1000 genomes]
rs7573334	0.82[EUR][1000 genomes]
rs7573583	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7575328	0.94[CEU][hapmap]
rs952034	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9941681	0.89[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623239	PDE11A	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178145000-178160200	Weak transcription	Adipose Nuclei	Adipose
2	chr2:178145600-178160200	Weak transcription	Aorta	Aorta
3	chr2:178146600-178180400	Weak transcription	Esophagus	oesophagus
4	chr2:178147400-178160000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:178147400-178160200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:178147600-178160400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:178147800-178163000	Weak transcription	Hela-S3	cervix
8	chr2:178147800-178187000	Weak transcription	HSMM	muscle
9	chr2:178147800-178190800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:178148800-178160000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:178148800-178160200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:178149000-178160200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:178150200-178160200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:178150200-178160200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:178151400-178167200	Weak transcription	Left Ventricle	heart
16	chr2:178151400-178179400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:178152000-178171200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:178152400-178160200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:178152800-178160200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:178152800-178178200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:178153200-178160200	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:178153200-178160200	Weak transcription	Ovary	ovary
23	chr2:178153200-178160200	Weak transcription	Stomach Mucosa	stomach
24	chr2:178155600-178160200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:178155600-178160400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:178155600-178174000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:178155800-178166600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:178155800-178167000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:178155800-178167400	Weak transcription	Primary B cells from cord blood	blood
30	chr2:178155800-178185200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:178156200-178160400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:178156400-178160000	Weak transcription	Liver	Liver
33	chr2:178156400-178160600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:178156400-178172000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:178156800-178160400	Weak transcription	GM12878-XiMat	blood
36	chr2:178156800-178160600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:178157600-178158200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:178157600-178158200	Enhancers	Fetal Intestine Small	intestine
39	chr2:178157600-178159600	Enhancers	HepG2	liver
40	chr2:178157800-178171600	Weak transcription	Primary T cells from cord blood	blood

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