Variant report

Variant	rs1060452
Chromosome Location	chr3:100040337-100040338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100036136..100038823-chr3:100040287..100043748,3	MCF-7	breast:
2	chr3:100028704..100030656-chr3:100038944..100041638,2	MCF-7	breast:
3	chr3:100038329..100040344-chr3:100052546..100054102,2	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11918291	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11920015	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11923373	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11924911	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486660	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486865	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12490043	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12490140	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492610	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12493917	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17335566	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17335614	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171205	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs277657	0.87[EUR][1000 genomes]
rs4928116	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4928117	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4928161	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4928166	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4928170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55950446	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56181320	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56311459	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57271189	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62281663	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6800780	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100053200	Weak transcription	Gastric	stomach
2	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
3	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
5	chr3:100007000-100045000	Weak transcription	Lung	lung
6	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
7	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:100014600-100042200	Weak transcription	Fetal Brain Male	brain
9	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:100019000-100043200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
12	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
14	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
16	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
18	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
20	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
22	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
23	chr3:100026400-100052800	Weak transcription	NHEK	skin
24	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:100029400-100041200	Weak transcription	Fetal Kidney	kidney
28	chr3:100029600-100053000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:100030200-100049800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:100030200-100053000	Weak transcription	Fetal Brain Female	brain
31	chr3:100031000-100053000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:100031200-100051200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:100033200-100046600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:100033600-100044600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:100033600-100045000	Weak transcription	Fetal Stomach	stomach
36	chr3:100033600-100052800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:100034600-100040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:100034800-100046600	Strong transcription	HSMM	muscle
39	chr3:100035000-100053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:100035600-100053000	Weak transcription	Stomach Mucosa	stomach
41	chr3:100036000-100052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:100036000-100053000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:100036200-100046600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:100036200-100047400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:100036200-100052800	Weak transcription	A549	lung
46	chr3:100036200-100053000	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:100036400-100041200	Strong transcription	Osteobl	bone
48	chr3:100036400-100046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:100036600-100046600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:100036800-100041000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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