Variant report

Variant	rs4240164
Chromosome Location	chr3:115706563-115706564
allele	C/T
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:60)

rs_ID	r²[population]
rs11918028	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12485818	0.93[CHD][hapmap];0.81[JPT][hapmap]
rs12495426	0.93[CHD][hapmap];0.81[JPT][hapmap]
rs13065579	0.81[JPT][hapmap]
rs13086615	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920382	0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1920383	0.93[CHD][hapmap];0.87[TSI][hapmap]
rs1920384	0.93[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs1920388	0.93[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2141626	0.81[JPT][hapmap]
rs2141629	0.81[JPT][hapmap]
rs35764849	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131452	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4131453	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4240163	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240165	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4286426	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4315682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4378955	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4398428	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4399891	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4426677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4518124	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4599302	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4831213	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831215	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831218	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831220	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4831221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831223	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438296	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs6776244	0.93[CHD][hapmap];0.81[JPT][hapmap]
rs6777196	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6787687	0.93[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6787872	0.86[ASW][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap]
rs6789600	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6790290	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6795318	0.94[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6804278	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807809	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7610371	0.93[CHD][hapmap];0.81[JPT][hapmap]
rs7625191	0.87[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs9289033	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289034	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289040	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs9813153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9815418	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9833319	0.86[EUR][1000 genomes]
rs9840787	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]
rs9848298	1.00[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap]
rs9850406	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863087	0.87[ASW][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs9869887	0.93[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9872913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873260	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878286	0.86[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
rs4240164	B4GALT4	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115700600-115711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:115701800-115708400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:115704400-115706600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:115705400-115709400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:115706000-115708600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:115706000-115713600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:115706200-115709000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:115706200-115709000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:115706200-115709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:115706200-115709000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:115706400-115708800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:115706400-115709000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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