Variant report

Variant	rs12625182
Chromosome Location	chr20:23604023-23604024
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23603693..23605548-chr20:23605615..23607306,2	MCF-7	breast:
2	chr20:23603350..23604972-chr20:23610943..23612814,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1010117	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1011226	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1064039	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1158167	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12624424	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625716	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710327	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13037490	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13038305	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13038337	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13038990	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13039536	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13040663	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13041070	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13043266	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13043610	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555355	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17751897	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016161	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2067488	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208289	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2254635	0.81[ASN][1000 genomes]
rs2405392	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2405393	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2424582	0.83[ASN][1000 genomes]
rs28703706	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3004139	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3004145	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3088162	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34374560	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34746357	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34792920	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34897231	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34911568	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35488434	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35573837	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35610040	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35782710	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35966482	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761280	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761281	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3787498	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3787499	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3810575	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3827141	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3827142	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3827143	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4346460	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4815222	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4815223	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4815224	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5030707	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55897275	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56077567	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56371840	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56388902	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57549987	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59059917	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036461	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036463	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036465	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036469	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036470	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036471	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036474	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6036476	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036478	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048920	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048922	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048923	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048924	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048925	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048926	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048928	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048929	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048933	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048936	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048937	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048939	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048941	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048945	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048946	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048949	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048950	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048952	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048956	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61035931	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6106685	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6114201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6114206	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6114208	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6114209	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6515375	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67567111	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67997662	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71334202	0.80[EUR][1000 genomes]
rs7265178	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7270413	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73318135	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs734801	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8114619	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115417	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8115423	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8116859	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8121147	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121283	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8121405	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs911119	0.89[EUR][1000 genomes];0.83[ASN][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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12625182	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23601800-23606000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:23601800-23606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:23602000-23609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:23602000-23610000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:23602000-23610200	Weak transcription	Lung	lung
7	chr20:23602000-23612200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr20:23602400-23606600	Weak transcription	Gastric	stomach
10	chr20:23603000-23606400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:23603200-23604200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:23603200-23604200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr20:23603200-23604800	Enhancers	Fetal Intestine Small	intestine
14	chr20:23603200-23605400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr20:23603400-23604200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:23603400-23604200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr20:23603400-23604200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr20:23603400-23604200	Enhancers	Fetal Intestine Large	intestine
19	chr20:23603400-23604200	Enhancers	Left Ventricle	heart
20	chr20:23603400-23604200	Active TSS	Right Atrium	heart
21	chr20:23603400-23604200	Active TSS	Stomach Smooth Muscle	stomach
22	chr20:23603400-23604200	Flanking Active TSS	HUVEC	blood vessel
23	chr20:23603400-23604200	Active TSS	NHDF-Ad	bronchial
24	chr20:23603400-23604200	Flanking Active TSS	NHEK	skin
25	chr20:23603400-23604200	Flanking Active TSS	Osteobl	bone
26	chr20:23603600-23604200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr20:23603600-23604200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:23603600-23604200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:23603600-23604200	Enhancers	Fetal Muscle Leg	muscle
30	chr20:23603600-23605000	Enhancers	K562	blood
31	chr20:23603800-23604200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr20:23603800-23604200	Flanking Active TSS	A549	lung
33	chr20:23603800-23604200	Flanking Active TSS	HMEC	breast
34	chr20:23603800-23604200	Flanking Active TSS	HSMM	muscle
35	chr20:23603800-23604200	Flanking Active TSS	NHLF	lung
36	chr20:23603800-23605800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr20:23603800-23606400	Weak transcription	Placenta	Placenta
38	chr20:23603800-23609200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr20:23603800-23609800	Weak transcription	Fetal Thymus	thymus
40	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr20:23604000-23604200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr20:23604000-23604200	Enhancers	Aorta	Aorta
43	chr20:23604000-23604200	Enhancers	Brain Anterior Caudate	brain
44	chr20:23604000-23604200	Enhancers	Brain Cingulate Gyrus	brain
45	chr20:23604000-23604200	Enhancers	Colon Smooth Muscle	Colon
46	chr20:23604000-23604200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr20:23604000-23604200	Active TSS	HSMMtube	muscle
48	chr20:23604000-23604200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr20:23604000-23604200	Active TSS	NH-A	brain
50	chr20:23604000-23604400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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