Variant report

Variant	rs9873580
Chromosome Location	chr3:159629367-159629368
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	chr3:159628184..159630550-chr3:159635946..159637758,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13324055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325119	1.00[ASN][1000 genomes]
rs1366303	1.00[ASN][1000 genomes]
rs1389817	1.00[ASN][1000 genomes]
rs28397084	1.00[ASN][1000 genomes]
rs28726382	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170508	1.00[ASN][1000 genomes]
rs73170509	1.00[ASN][1000 genomes]
rs73170513	1.00[ASN][1000 genomes]
rs73170516	1.00[ASN][1000 genomes]
rs9814871	1.00[ASN][1000 genomes]
rs9817922	1.00[ASN][1000 genomes]
rs9818736	1.00[ASN][1000 genomes]
rs9818907	1.00[ASN][1000 genomes]
rs9824156	1.00[ASN][1000 genomes]
rs9831512	1.00[ASN][1000 genomes]
rs9872563	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883824	1.00[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	nsv877698	chr3:159583518-159640152	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv997776	chr3:159585097-159668421	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3584505	chr3:159606945-159648615	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv4086	chr3:159612521-159657780	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159617000-159645000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:159617400-159631400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:159621200-159631600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:159627600-159629800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:159628600-159629400	Active TSS	Aorta	Aorta
6	chr3:159628600-159629400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:159628600-159629600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:159628600-159629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:159628800-159629400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:159628800-159629400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:159628800-159629400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:159628800-159629400	Active TSS	Primary T cells fromperipheralblood	blood
13	chr3:159628800-159629400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:159628800-159629400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:159628800-159629400	Active TSS	Brain Anterior Caudate	brain
16	chr3:159628800-159629400	Active TSS	Brain Cingulate Gyrus	brain
17	chr3:159628800-159629400	Active TSS	Brain Hippocampus Middle	brain
18	chr3:159628800-159629400	Active TSS	Brain Substantia Nigra	brain
19	chr3:159628800-159629400	Active TSS	Colon Smooth Muscle	Colon
20	chr3:159628800-159629400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:159628800-159629400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:159628800-159629400	Active TSS	Right Atrium	heart
23	chr3:159628800-159629400	Active TSS	NHLF	lung
24	chr3:159628800-159629600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:159628800-159629600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:159628800-159629600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:159628800-159629600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:159628800-159629600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:159628800-159629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:159628800-159629600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:159628800-159629600	Active TSS	Psoas Muscle	Psoas
32	chr3:159628800-159629600	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:159628800-159629600	Active TSS	HepG2	liver
34	chr3:159628800-159629600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr3:159628800-159629600	Flanking Active TSS	Osteobl	bone
36	chr3:159628800-159629800	Flanking Active TSS	Liver	Liver
37	chr3:159628800-159629800	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:159628800-159630000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:159629000-159629400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr3:159629000-159629400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:159629000-159629400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:159629000-159629400	Active TSS	Colonic Mucosa	Colon
43	chr3:159629000-159629400	Enhancers	Placenta	Placenta
44	chr3:159629000-159629400	Active TSS	Ovary	ovary
45	chr3:159629000-159629400	Active TSS	GM12878-XiMat	blood
46	chr3:159629000-159629400	Active TSS	HSMMtube	muscle
47	chr3:159629000-159629400	Active TSS	NHDF-Ad	bronchial
48	chr3:159629000-159629600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr3:159629000-159629600	Enhancers	Primary hematopoietic stem cells	blood
50	chr3:159629000-159629600	Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links