Variant report

Variant	rs28673478
Chromosome Location	chr3:43066017-43066018
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	chr3:43059886..43061659-chr3:43065331..43067767,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10470680	1.00[ASN][1000 genomes]
rs1392319	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403525	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074894	1.00[ASN][1000 genomes]
rs1816227	1.00[ASN][1000 genomes]
rs28378297	1.00[ASN][1000 genomes]
rs28601753	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915020	1.00[ASN][1000 genomes]
rs489117	1.00[ASN][1000 genomes]
rs530842	1.00[ASN][1000 genomes]
rs534284	1.00[ASN][1000 genomes]
rs551658	1.00[ASN][1000 genomes]
rs604393	1.00[ASN][1000 genomes]
rs61004728	1.00[ASN][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs62248962	1.00[ASN][1000 genomes]
rs62249006	1.00[ASN][1000 genomes]
rs62249007	1.00[ASN][1000 genomes]
rs62249008	1.00[ASN][1000 genomes]
rs62249009	1.00[ASN][1000 genomes]
rs62249011	1.00[ASN][1000 genomes]
rs62249013	1.00[ASN][1000 genomes]
rs62249014	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62249016	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651899	1.00[ASN][1000 genomes]
rs6763762	1.00[ASN][1000 genomes]
rs6773223	1.00[ASN][1000 genomes]
rs6775999	1.00[ASN][1000 genomes]
rs678310	1.00[ASN][1000 genomes]
rs6798412	1.00[ASN][1000 genomes]
rs680967	1.00[ASN][1000 genomes]
rs681341	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs735320	1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	1.00[ASN][1000 genomes]
rs7641452	1.00[ASN][1000 genomes]
rs7644923	1.00[ASN][1000 genomes]
rs9311330	1.00[ASN][1000 genomes]
rs9311331	1.00[ASN][1000 genomes]
rs9808932	1.00[ASN][1000 genomes]
rs9815609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816391	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824700	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833284	1.00[ASN][1000 genomes]
rs9837761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852930	1.00[ASN][1000 genomes]
rs9858270	1.00[ASN][1000 genomes]
rs9862469	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870478	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43053600-43073200	Weak transcription	Right Atrium	heart
2	chr3:43059600-43074400	Weak transcription	Lung	lung
3	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
4	chr3:43060800-43069600	Weak transcription	Stomach Mucosa	stomach
5	chr3:43061000-43066200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:43061000-43072200	Weak transcription	Liver	Liver
7	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:43061800-43073000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:43063000-43077400	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:43063400-43072000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:43063600-43072600	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:43064000-43077800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:43064400-43066600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:43064600-43066400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr3:43064600-43066400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:43064600-43066600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:43064600-43066600	Flanking Active TSS	Dnd41	blood
19	chr3:43064600-43066800	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:43064800-43066200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:43064800-43066200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:43064800-43066400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr3:43064800-43066400	Enhancers	Adipose Nuclei	Adipose
24	chr3:43064800-43067400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:43065000-43066400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:43065000-43066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:43065000-43067200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:43065200-43066400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:43065200-43067000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:43065200-43067000	Enhancers	Fetal Intestine Small	intestine
31	chr3:43065200-43072400	Weak transcription	Placenta	Placenta
32	chr3:43065400-43066200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:43065400-43067000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:43065600-43066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:43065800-43067000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:43065800-43067400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:43065800-43067800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:43065800-43067800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:43066000-43066200	Enhancers	Fetal Brain Male	brain
41	chr3:43066000-43066200	Flanking Active TSS	Thymus	Thymus
42	chr3:43066000-43066400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:43066000-43066400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr3:43066000-43066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:43066000-43066600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:43066000-43066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:43066000-43067200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:43066000-43068000	Enhancers	Fetal Thymus	thymus

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