Variant report

Variant	rs2874399
Chromosome Location	chr2:134245403-134245404
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	chr2:134245342..134247871-chr2:134256827..134259265,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1008125	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1017368	0.85[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11695605	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11887480	0.84[EUR][1000 genomes]
rs11896713	0.92[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs1836669	0.84[JPT][hapmap]
rs1865585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1897429	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2163653	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2163654	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2320935	0.98[EUR][1000 genomes]
rs3910163	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4954052	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4954059	0.81[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7559239	0.85[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7595258	0.96[EUR][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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2874399	RAB3GAP1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134235000-134247400	Weak transcription	Left Ventricle	heart
2	chr2:134239000-134247400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:134239600-134247600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:134240000-134262400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:134241800-134247200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:134242600-134246200	Enhancers	Fetal Muscle Leg	muscle
7	chr2:134243800-134245600	Enhancers	Brain Substantia Nigra	brain
8	chr2:134243800-134246200	Enhancers	Brain Hippocampus Middle	brain
9	chr2:134244000-134245600	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:134244200-134250400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:134244400-134245600	Enhancers	HSMMtube	muscle
12	chr2:134244400-134246000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:134244400-134246200	Enhancers	NHDF-Ad	bronchial
14	chr2:134244600-134245600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:134244600-134245600	Enhancers	Brain Anterior Caudate	brain
16	chr2:134244800-134252200	Weak transcription	Fetal Kidney	kidney
17	chr2:134245000-134247200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:134245200-134247200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:134245200-134247200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:134245200-134253000	Weak transcription	Fetal Stomach	stomach
21	chr2:134245400-134247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:134245400-134248600	Enhancers	Liver	Liver
23	chr2:134245400-134251400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:134245400-134253000	Weak transcription	Brain Inferior Temporal Lobe	brain

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