Variant report

Variant	rs1399829
Chromosome Location	chr5:127138600-127138601
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	chr5:127130582..127132988-chr5:127136940..127138622,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10519960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241942	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11950864	0.84[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11957799	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228156	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12653785	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515640	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1849938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1897525	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569146	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569148	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2673772	0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57883466	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59513079	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs790827	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs812059	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127135200-127143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:127136600-127138800	Enhancers	NHLF	lung
3	chr5:127136600-127139200	Enhancers	Stomach Mucosa	stomach
4	chr5:127137000-127138800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:127137000-127139000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:127137000-127139000	Enhancers	HUVEC	blood vessel
7	chr5:127137200-127139000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:127137400-127139200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:127137600-127139000	Enhancers	Stomach Smooth Muscle	stomach
10	chr5:127137800-127138600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:127137800-127138600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:127138000-127138800	Enhancers	Fetal Lung	lung
13	chr5:127138200-127138600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:127138200-127138800	Enhancers	NHDF-Ad	bronchial
15	chr5:127138200-127140000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:127138200-127140200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:127138200-127140400	Weak transcription	NHEK	skin
18	chr5:127138200-127140600	Weak transcription	HSMM	muscle
19	chr5:127138200-127140600	Weak transcription	HSMMtube	muscle
20	chr5:127138400-127138600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:127138400-127138600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr5:127138400-127139000	Weak transcription	Aorta	Aorta
23	chr5:127138400-127139200	Enhancers	Osteobl	bone
24	chr5:127138400-127139800	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:127138400-127140000	Weak transcription	NH-A	brain
26	chr5:127138400-127140400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:127138400-127141400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:127138400-127141800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:127138600-127140600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:127138600-127140600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:127138600-127140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:127138600-127146400	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