Variant report

Variant	rs1865585
Chromosome Location	chr2:134238128-134238129
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.98[EUR][1000 genomes]
rs1017368	0.85[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.83[EUR][1000 genomes]
rs11695605	0.96[CEU][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11887480	0.84[EUR][1000 genomes]
rs11896713	0.92[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs1836669	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1897429	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2163653	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2163654	0.85[CEU][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2320935	0.98[EUR][1000 genomes]
rs2874399	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]
rs3910163	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4954052	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4954059	0.81[CEU][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7559239	0.85[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.83[EUR][1000 genomes]
rs7595258	0.95[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
rs1865585	RAB3GAP1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134231400-134240000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:134235000-134244400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:134235000-134247400	Weak transcription	Left Ventricle	heart
4	chr2:134235200-134238400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:134235200-134240600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:134236200-134238200	Weak transcription	HMEC	breast
7	chr2:134237800-134239200	Enhancers	NHEK	skin
8	chr2:134238000-134238600	Enhancers	Liver	Liver
9	chr2:134238000-134239200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:134238000-134239200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:134238000-134239600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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