Variant report

Variant	rs9289040
Chromosome Location	chr3:115778365-115778366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11918028	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12485818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13100598	0.81[ASN][1000 genomes]
rs1920382	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920383	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920384	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920385	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920388	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2141626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2141627	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2141629	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240164	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs4240166	0.80[JPT][hapmap]
rs4286426	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs4398428	0.81[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.81[EUR][1000 genomes]
rs4399891	0.86[JPT][hapmap]
rs4426677	0.81[JPT][hapmap]
rs4518124	0.90[CHD][hapmap]
rs4611819	0.90[CHD][hapmap]
rs4831218	0.86[CHD][hapmap]
rs4831219	0.90[CHD][hapmap]
rs4831221	0.81[JPT][hapmap]
rs4831222	0.81[JPT][hapmap]
rs6438296	0.84[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes]
rs6776244	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787687	0.81[CEU][hapmap];0.90[CHD][hapmap];0.83[EUR][1000 genomes]
rs6787872	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6795318	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6807809	0.84[CEU][hapmap]
rs7610371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7625191	0.83[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes]
rs7632252	0.86[EUR][1000 genomes]
rs9289034	0.86[CHD][hapmap]
rs9289039	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813153	0.81[JPT][hapmap]
rs9840787	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs9845521	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9848298	0.81[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9863087	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9869887	0.88[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9872913	0.81[JPT][hapmap]
rs9878286	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1001538	chr3:115746561-115791116	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115766200-115794200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:115775800-115779400	Enhancers	HMEC	breast
3	chr3:115776800-115778400	Weak transcription	GM12878-XiMat	blood
4	chr3:115776800-115778800	Enhancers	NHEK	skin
5	chr3:115777000-115779000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:115777000-115779000	Enhancers	K562	blood
7	chr3:115777200-115778400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:115777200-115778600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:115777800-115779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:115778000-115778400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr3:115778000-115778400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:115778000-115779200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:115778000-115779200	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:115778200-115778800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:115778200-115779000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:115778200-115779000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:115778200-115779000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:115778200-115779000	Enhancers	Colon Smooth Muscle	Colon
19	chr3:115778200-115779200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:115778200-115779200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:115778200-115779400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:115778200-115779400	Enhancers	Hela-S3	cervix
23	chr3:115778200-115779400	Enhancers	NHDF-Ad	bronchial
24	chr3:115778200-115779600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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