Variant report

Variant	rs12492540
Chromosome Location	chr3:50692835-50692836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50690479..50693094-chr3:50743826..50746673,2	K562	blood:
2	chr3:50690938..50693728-chr3:50694642..50698811,4	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1077215	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12486143	0.85[AMR][1000 genomes]
rs12486717	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487817	0.83[AMR][1000 genomes]
rs12487821	0.83[AFR][1000 genomes]
rs12489607	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491440	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491812	0.88[AMR][1000 genomes]
rs12492093	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494094	0.90[AMR][1000 genomes]
rs12494326	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12495399	0.86[ASN][1000 genomes]
rs17050991	0.88[AMR][1000 genomes]
rs17050995	0.85[AMR][1000 genomes]
rs17051000	0.90[AMR][1000 genomes]
rs17051043	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051045	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051403	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872184	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2035484	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2076927	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170840	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227292	0.87[ASN][1000 genomes]
rs2227293	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239750	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239751	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239753	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3749265	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3752449	0.87[ASN][1000 genomes]
rs3792323	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4476497	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688695	0.83[AFR][1000 genomes]
rs4688705	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688707	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688709	0.87[ASN][1000 genomes]
rs4688710	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688713	0.85[AMR][1000 genomes]
rs4688716	0.81[AMR][1000 genomes]
rs56170012	0.83[AMR][1000 genomes]
rs56856095	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57910827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58427389	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58529408	0.91[ASN][1000 genomes]
rs59036236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60552073	0.90[AMR][1000 genomes]
rs60552386	0.82[ASN][1000 genomes]
rs60602904	0.80[ASN][1000 genomes]
rs60877431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61193866	0.88[AMR][1000 genomes]
rs61316441	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61574029	0.87[AMR][1000 genomes]
rs61613532	0.87[AMR][1000 genomes]
rs616689	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446208	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650655	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6766638	0.83[AMR][1000 genomes]
rs6771348	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783922	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794155	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72938758	0.87[AMR][1000 genomes]
rs72940708	0.83[EUR][1000 genomes]
rs72942785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72944726	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944730	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73835531	0.85[AMR][1000 genomes]
rs743753	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745356	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762889	0.87[ASN][1000 genomes]
rs808148	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs876103	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs876104	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876105	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868889	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9879397	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
2	chr3:50685400-50693000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:50685400-50693000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:50685800-50703800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:50687000-50696400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:50687000-50712000	Weak transcription	Right Atrium	heart
7	chr3:50687200-50693000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:50687400-50695600	Weak transcription	HMEC	breast
9	chr3:50687600-50694200	Weak transcription	Lung	lung
10	chr3:50687600-50697400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:50687600-50702400	Weak transcription	Spleen	Spleen
12	chr3:50688000-50693600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:50688200-50702600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:50688800-50702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:50689000-50693600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:50690200-50702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:50690400-50694400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:50690400-50700200	Weak transcription	Left Ventricle	heart
19	chr3:50691600-50693000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:50691800-50693000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:50691800-50693000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:50691800-50693200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:50692000-50693000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:50692000-50693000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:50692000-50693000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:50692000-50693200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:50692000-50693200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:50692000-50693200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:50692200-50693000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:50692200-50693000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:50692200-50693000	Enhancers	NHEK	skin
32	chr3:50692400-50693000	Weak transcription	Esophagus	oesophagus
33	chr3:50692400-50693200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:50692600-50693000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:50692600-50693000	Enhancers	Fetal Thymus	thymus
36	chr3:50692800-50693000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:50692800-50693000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:50692800-50693000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:50692800-50693000	Enhancers	Fetal Muscle Leg	muscle
40	chr3:50692800-50693200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:50692800-50693200	Enhancers	Right Ventricle	heart
42	chr3:50692800-50695600	Weak transcription	HSMM	muscle
43	chr3:50692800-50700600	Weak transcription	NHDF-Ad	bronchial

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