Variant report

Variant	rs60235167
Chromosome Location	chr3:119808256-119808257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119707707..119709811-chr3:119807417..119810335,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10433404	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934502	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10934503	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934505	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934506	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934507	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11915717	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12054090	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12108149	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629015	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12630829	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632325	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12634476	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634889	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12635018	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12638973	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1574154	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1870931	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980718	0.81[ASN][1000 genomes]
rs28831519	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4340737	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4688042	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4688046	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688047	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688053	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688054	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4688059	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58863896	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264714	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62264734	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62264739	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264747	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62264749	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266274	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266277	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266281	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797459	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7639388	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:119788400-119808600	Weak transcription	Primary B cells from cord blood	blood
4	chr3:119789400-119809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:119790600-119809200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:119790800-119809200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:119790800-119809400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:119791000-119809600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:119798400-119809400	Weak transcription	Lung	lung
10	chr3:119799000-119810400	Weak transcription	Placenta	Placenta
11	chr3:119799200-119810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:119799800-119809400	Weak transcription	HSMM	muscle
13	chr3:119804200-119809200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:119804600-119812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:119804600-119812000	Weak transcription	Pancreas	Pancrea
16	chr3:119804800-119809200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:119805200-119809200	Weak transcription	NH-A	brain
18	chr3:119805600-119809200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:119805600-119810600	Weak transcription	Stomach Mucosa	stomach
20	chr3:119805600-119812000	Weak transcription	Gastric	stomach
21	chr3:119805800-119811400	Weak transcription	Esophagus	oesophagus
22	chr3:119806000-119809200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:119806800-119809600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:119807000-119809600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:119807200-119809000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:119807400-119808400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:119807400-119808400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:119807400-119808400	Enhancers	Brain Hippocampus Middle	brain
29	chr3:119807400-119808400	Enhancers	HepG2	liver
30	chr3:119807400-119808600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:119807400-119809200	Enhancers	Primary T cells from cord blood	blood
32	chr3:119807400-119809200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:119807400-119809200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:119807400-119809400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:119807400-119809600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr3:119807600-119808400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:119807600-119808400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:119807600-119808400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:119807600-119808400	Enhancers	Brain Anterior Caudate	brain
40	chr3:119807600-119808400	Enhancers	Fetal Intestine Large	intestine
41	chr3:119807600-119808400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:119807600-119808400	Genic enhancers	A549	lung
43	chr3:119807600-119808600	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:119807600-119808600	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr3:119807600-119808600	Enhancers	Fetal Kidney	kidney
46	chr3:119807600-119808800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:119807600-119809200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:119807600-119809600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:119807600-119809600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr3:119807600-119809600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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