Variant report

Variant	rs9840787
Chromosome Location	chr3:115695120-115695121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11918028	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12485818	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs12495426	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs13065579	0.81[JPT][hapmap]
rs13086615	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1920382	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs1920383	0.89[CHD][hapmap]
rs1920384	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs1920388	0.94[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap]
rs2141626	0.81[JPT][hapmap]
rs2141629	0.81[JPT][hapmap]
rs35764849	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131452	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4131453	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4240163	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240164	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240165	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4286426	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4315682	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4378955	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4398428	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs4399891	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4426677	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4518124	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4599302	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4611819	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4831213	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4831215	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4831218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831219	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831220	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4831221	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4831222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4831223	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438296	0.94[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs6776244	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs6777196	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787687	0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6787872	0.96[CHD][hapmap];0.87[JPT][hapmap]
rs6789600	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6790290	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6795318	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs6804278	0.94[ASN][1000 genomes]
rs6807809	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7610371	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs7625191	0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs9289033	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9289034	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9289040	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs9813153	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815418	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848298	0.96[CHD][hapmap];0.87[JPT][hapmap]
rs9850406	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863087	0.96[CHD][hapmap];0.87[JPT][hapmap]
rs9869887	0.81[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs9872913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873260	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878286	0.82[CHD][hapmap];0.81[JPT][hapmap]

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	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv591344	chr3:115672480-115704434	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840787	B4GALT4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115688000-115695400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:115693400-115695200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:115694200-115695600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:115694200-115702800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:115694400-115695800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:115694600-115695200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:115694600-115695400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:115695000-115695200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:115695000-115695400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:115695000-115699600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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