Variant report

Variant	rs12405779
Chromosome Location	chr1:227008502-227008503
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227006518..227010110-chr1:227013321..227015905,5	K562	blood:
2	chr1:227005486..227010136-chr1:227013017..227015365,4	K562	blood:
3	chr1:227001349..227004344-chr1:227005535..227008816,3	MCF-7	breast:
4	chr1:226888820..226891466-chr1:227007435..227009237,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10799367	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916057	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916059	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11580744	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11582528	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11588886	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12119853	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12123818	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12125811	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127440	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130732	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12132893	0.93[JPT][hapmap]
rs12138310	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143886	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403248	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733650	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12747261	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12760155	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16846644	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1794035	0.81[CEU][hapmap]
rs1800672	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1800673	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1800681	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236912	0.86[EUR][1000 genomes]
rs3213436	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34081886	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35029375	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35213802	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35396772	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35519961	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35744376	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820649	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3829979	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6426550	0.82[EUR][1000 genomes]
rs6426554	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676065	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676067	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6680780	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71648404	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs732479	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7512804	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12405779	PSEN2	cis	cerebellum	SCAN
rs12405779	PSEN2	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226995800-227009800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:227003400-227008600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:227003400-227008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:227003400-227008600	Weak transcription	Brain Angular Gyrus	brain
5	chr1:227003400-227008600	Weak transcription	HSMM	muscle
6	chr1:227003400-227008600	Weak transcription	HSMMtube	muscle
7	chr1:227003400-227008800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:227003400-227009200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:227003400-227009200	Weak transcription	Right Ventricle	heart
10	chr1:227003400-227009400	Weak transcription	Small Intestine	intestine
11	chr1:227003400-227015000	Weak transcription	Thymus	Thymus
12	chr1:227003600-227008800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:227003600-227008800	Weak transcription	Psoas Muscle	Psoas
14	chr1:227003600-227009200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:227004000-227008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:227004000-227009200	Weak transcription	Esophagus	oesophagus
17	chr1:227004000-227009400	Weak transcription	Fetal Thymus	thymus
18	chr1:227004200-227008600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:227004200-227008600	Weak transcription	Fetal Intestine Small	intestine
20	chr1:227004200-227009000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:227004200-227011400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:227005000-227008600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:227005000-227008600	Weak transcription	HMEC	breast
24	chr1:227005000-227008800	Weak transcription	NHEK	skin
25	chr1:227005000-227009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:227005200-227008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:227005200-227008600	Weak transcription	NH-A	brain
28	chr1:227005200-227008800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:227005200-227009200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:227006800-227010800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:227007000-227008600	Enhancers	Placenta	Placenta
32	chr1:227007000-227009600	Enhancers	Hela-S3	cervix
33	chr1:227007000-227010000	Enhancers	Adipose Nuclei	Adipose
34	chr1:227007200-227010200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:227007200-227011600	Enhancers	Fetal Stomach	stomach
36	chr1:227007400-227010000	Enhancers	HUVEC	blood vessel
37	chr1:227007400-227012000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:227007600-227008800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:227007800-227010200	Enhancers	Brain Substantia Nigra	brain
40	chr1:227007800-227010200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:227007800-227010600	Enhancers	Fetal Muscle Leg	muscle
42	chr1:227008000-227009400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:227008000-227009600	Enhancers	Fetal Kidney	kidney
44	chr1:227008000-227009800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:227008000-227010000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:227008000-227010000	Enhancers	Brain Cingulate Gyrus	brain
47	chr1:227008000-227010200	Enhancers	NHDF-Ad	bronchial
48	chr1:227008000-227010800	Enhancers	Brain Hippocampus Middle	brain
49	chr1:227008200-227008600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:227008200-227008600	Weak transcription	Right Atrium	heart

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