Variant report

Variant	rs1897432
Chromosome Location	chr2:134276760-134276761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr2:134276225-134276818	Hela-S3	cervix:	n/a	n/a
2	EBF1	chr2:134276676-134276840	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
NCKAP5	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1017365	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682672	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1368092	0.82[TSI][hapmap]
rs1368093	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs1432285	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1432286	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1432287	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1812081	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1816384	0.82[TSI][hapmap]
rs1821182	0.84[EUR][1000 genomes]
rs1835816	0.82[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1835817	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966628	0.82[CEU][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4954060	0.81[EUR][1000 genomes]
rs4954061	0.84[EUR][1000 genomes]
rs56049516	0.84[EUR][1000 genomes]
rs6430424	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6430425	0.82[EUR][1000 genomes]
rs6711103	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6750306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930195	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs930196	0.82[CEU][hapmap];0.84[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	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
4	esv2830192	chr2:134259612-134311713	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1897432	RAB3GAP1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134268200-134290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134274200-134281600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:134274600-134276800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:134275600-134279600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:134276000-134276800	Weak transcription	NHLF	lung
6	chr2:134276200-134277200	Enhancers	NHDF-Ad	bronchial
7	chr2:134276200-134277400	Enhancers	Hela-S3	cervix
8	chr2:134276600-134276800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:134276600-134277200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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