Variant report

Variant	rs12312552
Chromosome Location	chr12:42554466-42554467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42548352..42550645-chr12:42552454..42554810,2	MCF-7	breast:
2	chr12:42552974..42555837-chr12:42630405..42632767,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10437938	0.82[AFR][1000 genomes]
rs11181316	1.00[AMR][1000 genomes]
rs11181323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11181352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11181358	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11181365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12298117	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299325	1.00[AMR][1000 genomes]
rs12300748	1.00[AMR][1000 genomes]
rs12300940	1.00[AMR][1000 genomes]
rs12306689	1.00[AMR][1000 genomes]
rs12306988	1.00[AMR][1000 genomes]
rs12308498	0.94[AFR][1000 genomes]
rs12310121	1.00[AMR][1000 genomes]
rs12310800	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313439	1.00[AMR][1000 genomes]
rs12313898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319636	1.00[ASW][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs12320539	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12322282	1.00[AMR][1000 genomes]
rs12322316	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12322344	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12322394	1.00[AMR][1000 genomes]
rs12385814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28431054	1.00[AMR][1000 genomes]
rs28599887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56736670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58977672	1.00[AMR][1000 genomes]
rs61023006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6582387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6582388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7137140	0.94[AFR][1000 genomes]
rs7306048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7959000	1.00[AMR][1000 genomes]
rs7971397	1.00[AMR][1000 genomes]
rs7974036	1.00[AMR][1000 genomes]
rs7976241	1.00[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
4	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
7	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
9	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
12	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
13	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
14	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine
15	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain
16	chr12:42546000-42564400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:42547200-42563800	Weak transcription	Fetal Stomach	stomach
18	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:42549400-42575000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:42550200-42555400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:42550400-42556200	Weak transcription	Fetal Heart	heart
22	chr12:42550600-42555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:42550600-42557400	Weak transcription	Colonic Mucosa	Colon
24	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:42550800-42555600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:42550800-42568400	Weak transcription	Right Ventricle	heart
27	chr12:42551400-42554800	Strong transcription	Primary B cells from cord blood	blood
28	chr12:42551400-42557800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:42551600-42555200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:42551800-42555200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:42551800-42555400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:42551800-42555400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:42551800-42555400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:42551800-42555600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:42552000-42556000	Weak transcription	HMEC	breast
36	chr12:42552000-42604000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:42552200-42554800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:42552200-42555000	Strong transcription	HSMM	muscle
39	chr12:42552200-42555400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:42552200-42555800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:42552200-42557400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:42552200-42574800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:42552200-42591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:42552200-42613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:42552400-42555600	Strong transcription	Dnd41	blood
46	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
47	chr12:42552600-42578800	Weak transcription	Lung	lung
48	chr12:42552800-42556000	Weak transcription	NHLF	lung
49	chr12:42552800-42564400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:42553000-42555000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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