Variant report

Variant	rs60294656
Chromosome Location	chr3:142503278-142503279
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	chr3:142499960..142502376-chr3:142502794..142505025,2	MCF-7	breast:
2	chr3:142502229..142505111-chr3:142507605..142510534,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1132030	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11715459	0.81[ASN][1000 genomes]
rs11717993	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915805	0.90[ASN][1000 genomes]
rs1382688	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871349	0.91[EUR][1000 genomes]
rs2033912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2049328	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2177398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2354856	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524951	0.84[EUR][1000 genomes]
rs28658009	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661660	0.91[EUR][1000 genomes]
rs28689551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34076811	0.91[EUR][1000 genomes]
rs34445140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35467195	0.89[ASN][1000 genomes]
rs35862982	0.90[ASN][1000 genomes]
rs3821647	0.86[EUR][1000 genomes]
rs4259003	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4530572	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs45497994	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4643748	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55722370	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56666685	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56775607	0.90[ASN][1000 genomes]
rs57026466	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59108985	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60319320	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60752859	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440106	0.87[ASN][1000 genomes]
rs6440108	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440110	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66897945	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772222	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6777466	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791501	0.91[EUR][1000 genomes]
rs6798849	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803681	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6807862	0.90[EUR][1000 genomes]
rs73232711	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621642	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7622662	0.84[EUR][1000 genomes]
rs7623977	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631245	0.80[EUR][1000 genomes]
rs7635768	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7637826	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7637846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638459	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639403	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641514	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642332	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646197	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653309	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7772	0.91[EUR][1000 genomes]
rs936339	0.83[EUR][1000 genomes]
rs953239	0.87[ASN][1000 genomes]
rs9754885	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9758429	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784320	0.81[EUR][1000 genomes]
rs9815607	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824476	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9835135	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836269	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9841007	0.81[EUR][1000 genomes]
rs9846406	0.81[EUR][1000 genomes]
rs9849461	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850734	0.84[EUR][1000 genomes]
rs9851381	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9864230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9868886	0.99[EUR][1000 genomes];0.92[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	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142467800-142503400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:142468200-142511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142468200-142525200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:142468400-142508800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:142468400-142525200	Weak transcription	Fetal Brain Male	brain
6	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
7	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
8	chr3:142468600-142525200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:142468800-142513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:142470600-142505800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:142472400-142509800	Weak transcription	HepG2	liver
12	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:142484600-142506400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:142487400-142513600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:142487600-142503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:142487800-142506800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:142488800-142505000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:142490000-142503600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142490200-142529400	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:142490400-142522800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:142490800-142507400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:142495400-142527000	Weak transcription	Brain Angular Gyrus	brain
24	chr3:142497600-142509000	Weak transcription	A549	lung
25	chr3:142497600-142514200	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:142498600-142517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:142498600-142522800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:142498600-142526800	Weak transcription	Osteobl	bone
29	chr3:142498800-142503400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:142499000-142527000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:142499400-142547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:142501400-142508600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:142501600-142504800	Weak transcription	Fetal Intestine Large	intestine
34	chr3:142501600-142525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:142501600-142525600	Weak transcription	Fetal Stomach	stomach
36	chr3:142501800-142518400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:142501800-142521400	Weak transcription	Ovary	ovary
38	chr3:142501800-142527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:142501800-142528000	Weak transcription	Left Ventricle	heart
40	chr3:142501800-142535600	Weak transcription	Aorta	Aorta
41	chr3:142502000-142511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:142502000-142514000	Weak transcription	HSMM	muscle
43	chr3:142502000-142521400	Weak transcription	Adipose Nuclei	Adipose
44	chr3:142502000-142529400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:142502200-142505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:142502400-142514200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:142502400-142522800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:142502600-142505000	Weak transcription	Placenta	Placenta
49	chr3:142503200-142504200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:142503200-142506600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links