Variant report

Variant	rs12120428
Chromosome Location	chr1:150403238-150403239
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150336165..150339501-chr1:150400580..150403941,7	MCF-7	breast:
2	chr1:150335854..150339883-chr1:150398691..150403963,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163125	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11204665	1.00[AFR][1000 genomes]
rs11205367	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11205374	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11205377	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11576289	1.00[AFR][1000 genomes]
rs11576293	1.00[AFR][1000 genomes]
rs11577751	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11578585	1.00[AFR][1000 genomes]
rs11579341	1.00[AFR][1000 genomes]
rs11580764	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11582835	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11586880	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11587682	1.00[AFR][1000 genomes]
rs11587837	1.00[AFR][1000 genomes]
rs11588221	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12119320	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12120867	1.00[AFR][1000 genomes]
rs12126312	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12128385	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12132918	1.00[AFR][1000 genomes]
rs12134682	0.81[AMR][1000 genomes]
rs12138453	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12142331	1.00[AFR][1000 genomes]
rs12142874	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12144958	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2133128	1.00[AFR][1000 genomes]
rs34848955	1.00[AFR][1000 genomes]
rs41264469	1.00[AFR][1000 genomes]
rs41273537	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41300865	1.00[AFR][1000 genomes]
rs4265470	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55973252	1.00[AFR][1000 genomes]
rs72696841	1.00[AFR][1000 genomes]
rs72696848	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72696852	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72696855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72696859	0.86[EUR][1000 genomes]
rs72696873	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72696880	1.00[AFR][1000 genomes]
rs72696901	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72698822	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72698842	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72698892	1.00[AFR][1000 genomes]
rs72700804	1.00[AFR][1000 genomes]
rs72700810	1.00[AFR][1000 genomes]
rs72700813	1.00[AFR][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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150338400-150405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:150340000-150416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:150362600-150416600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:150370000-150407800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:150373200-150442800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:150380600-150429800	Weak transcription	Aorta	Aorta
7	chr1:150381200-150414400	Weak transcription	Fetal Brain Female	brain
8	chr1:150381800-150417400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:150382000-150418200	Weak transcription	Colonic Mucosa	Colon
10	chr1:150382000-150432400	Weak transcription	Fetal Brain Male	brain
11	chr1:150382400-150407800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:150382600-150414400	Weak transcription	Lung	lung
13	chr1:150382800-150412800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:150382800-150414600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:150382800-150414800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:150383000-150416600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:150383400-150413800	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:150383400-150414000	Weak transcription	NH-A	brain
19	chr1:150383400-150414200	Weak transcription	Left Ventricle	heart
20	chr1:150383400-150414200	Weak transcription	Osteobl	bone
21	chr1:150383400-150419000	Weak transcription	Fetal Kidney	kidney
22	chr1:150383400-150419000	Weak transcription	Gastric	stomach
23	chr1:150383400-150432200	Weak transcription	Right Ventricle	heart
24	chr1:150383400-150443200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:150383600-150416800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:150383600-150418200	Weak transcription	Pancreas	Pancrea
27	chr1:150385000-150407800	Weak transcription	HepG2	liver
28	chr1:150385600-150415000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:150386800-150429800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:150387000-150414600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:150387000-150414800	Weak transcription	Brain Germinal Matrix	brain
32	chr1:150388600-150416600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:150388600-150416600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:150388600-150416800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:150388800-150408000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:150388800-150413800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:150389400-150423400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:150389600-150405600	Strong transcription	Dnd41	blood
39	chr1:150389600-150417000	Weak transcription	HMEC	breast
40	chr1:150390000-150429600	Weak transcription	A549	lung
41	chr1:150390200-150416400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:150391600-150414400	Weak transcription	Ovary	ovary
43	chr1:150391600-150416800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:150391800-150414200	Weak transcription	Placenta	Placenta
45	chr1:150391800-150416800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:150392600-150409200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:150392600-150410800	Weak transcription	Thymus	Thymus
48	chr1:150392600-150418400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:150392800-150413800	Weak transcription	Fetal Lung	lung
50	chr1:150392800-150414200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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