Variant report

Variant	rs2453469
Chromosome Location	chr12:49219569-49219570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49217312..49223334-chr12:49223804..49229177,10	MCF-7	breast:
2	chr12:49207192..49209102-chr12:49218878..49220793,2	MCF-7	breast:
3	chr12:49218446..49220087-chr12:49244842..49246602,2	K562	blood:
4	chr12:49217911..49220873-chr12:49258155..49260990,2	K562	blood:
5	chr12:49208067..49210206-chr12:49219385..49222267,2	K562	blood:
6	chr12:49211648..49214414-chr12:49216563..49220166,3	K562	blood:

Variant related genes	Relation type
ENSG00000167535	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1057908	0.83[LWK][hapmap]
rs10875877	0.84[AMR][1000 genomes]
rs10875878	0.90[ASN][1000 genomes]
rs1532365	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2070615	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2446989	0.84[AMR][1000 genomes]
rs2446992	0.84[AMR][1000 genomes]
rs2453468	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453478	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2860360	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2926803	0.84[AMR][1000 genomes]
rs2926804	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes]
rs3101344	0.83[AMR][1000 genomes]
rs4760643	0.83[AMR][1000 genomes]
rs6580695	0.85[JPT][hapmap]
rs7164	0.85[JPT][hapmap]
rs903568	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs931570	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2453469	GPD1	cis	parietal	SCAN
rs2453469	AMIGO2	cis	parietal	SCAN
rs2453469	DNAJC22	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49212600-49223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:49212800-49224000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:49213000-49220000	Weak transcription	NHEK	skin
4	chr12:49213000-49220200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:49213000-49221200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:49213000-49221600	Weak transcription	Left Ventricle	heart
7	chr12:49213000-49222400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:49213000-49222800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:49213000-49223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:49213000-49226000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:49213000-49231200	Weak transcription	Right Atrium	heart
12	chr12:49213200-49220000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:49213200-49220000	Weak transcription	Lung	lung
14	chr12:49213200-49220000	Weak transcription	NH-A	brain
15	chr12:49213200-49220000	Weak transcription	Osteobl	bone
16	chr12:49213200-49220600	Weak transcription	A549	lung
17	chr12:49213200-49220800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:49213200-49221000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:49213200-49221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:49213200-49222400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:49213200-49222800	Weak transcription	Hela-S3	cervix
22	chr12:49213200-49223200	Weak transcription	HSMMtube	muscle
23	chr12:49213200-49223800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:49213200-49223800	Weak transcription	HSMM	muscle
25	chr12:49213400-49220000	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:49213400-49220000	Weak transcription	Spleen	Spleen
27	chr12:49213400-49220000	Weak transcription	HUVEC	blood vessel
28	chr12:49213400-49220200	Weak transcription	Right Ventricle	heart
29	chr12:49213400-49220400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:49213400-49221800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:49213400-49222200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:49213400-49222600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:49213400-49224800	Weak transcription	Fetal Kidney	kidney
34	chr12:49213400-49226000	Weak transcription	Psoas Muscle	Psoas
35	chr12:49213600-49220800	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:49213600-49221800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:49214000-49220800	Weak transcription	Brain Anterior Caudate	brain
38	chr12:49214200-49220000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:49214200-49220000	Weak transcription	Fetal Thymus	thymus
40	chr12:49214400-49220200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:49214400-49220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:49214400-49221000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:49214600-49220200	Weak transcription	Fetal Lung	lung
44	chr12:49214600-49221000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:49214600-49234800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:49215200-49243800	Strong transcription	Fetal Stomach	stomach
47	chr12:49215400-49235400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:49215600-49240000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:49215800-49235000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:49216200-49235400	Strong transcription	Fetal Muscle Leg	muscle

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