Variant report

Variant	rs17473484
Chromosome Location	chr5:114915460-114915461
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	chr5:114908239..114910015-chr5:114914437..114916676,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11740361	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1427860	0.84[EUR][1000 genomes]
rs17137925	1.00[CHB][hapmap]
rs17137978	0.84[EUR][1000 genomes]
rs17393505	0.81[EUR][1000 genomes]
rs17395548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395582	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472256	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17472710	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17473708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473792	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474216	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2194114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776801	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776802	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73253029	0.94[ASN][1000 genomes]
rs7712026	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:114907800-114918200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:114908200-114918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:114908800-114918600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:114909000-114918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:114909000-114919200	Weak transcription	Left Ventricle	heart
7	chr5:114909000-114919200	Weak transcription	Psoas Muscle	Psoas
8	chr5:114910200-114918400	Weak transcription	Fetal Intestine Large	intestine
9	chr5:114910400-114925200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:114910400-114929400	Weak transcription	Adipose Nuclei	Adipose
11	chr5:114910800-114916600	Weak transcription	Ovary	ovary
12	chr5:114911200-114935600	Weak transcription	Gastric	stomach
13	chr5:114911400-114917000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:114911600-114918600	Weak transcription	HSMMtube	muscle
15	chr5:114911800-114922400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:114912000-114924600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:114912200-114918600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:114912200-114919200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:114912200-114919200	Weak transcription	HMEC	breast
20	chr5:114912200-114920400	Weak transcription	NHEK	skin
21	chr5:114912200-114921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:114912400-114915800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:114912600-114916400	Weak transcription	NHLF	lung
24	chr5:114912600-114919200	Weak transcription	HUVEC	blood vessel
25	chr5:114913000-114935200	Weak transcription	Aorta	Aorta
26	chr5:114913600-114916400	Enhancers	Primary B cells from peripheral blood	blood
27	chr5:114913600-114924400	Weak transcription	Placenta	Placenta
28	chr5:114913800-114917600	Strong transcription	HSMM	muscle
29	chr5:114913800-114919200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:114913800-114921000	Weak transcription	Fetal Lung	lung
31	chr5:114914000-114916200	Weak transcription	Primary T cells from cord blood	blood
32	chr5:114914400-114915600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:114914400-114915600	Enhancers	Brain Substantia Nigra	brain
34	chr5:114914400-114916400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:114914400-114936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:114914600-114916000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:114914600-114917400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr5:114914800-114915600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:114914800-114915800	Flanking Active TSS	GM12878-XiMat	blood
40	chr5:114914800-114916400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:114914800-114937400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:114915000-114915600	Enhancers	Brain Hippocampus Middle	brain
43	chr5:114915000-114915600	Genic enhancers	NH-A	brain
44	chr5:114915000-114915800	Enhancers	A549	lung
45	chr5:114915000-114916000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:114915000-114916800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:114915000-114917000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:114915000-114917000	Genic enhancers	Osteobl	bone
49	chr5:114915000-114917600	Genic enhancers	NHDF-Ad	bronchial
50	chr5:114915200-114915600	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links