Variant report

Variant	rs6803846
Chromosome Location	chr3:120028644-120028645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070508	1.00[ASN][1000 genomes]
rs13073885	1.00[JPT][hapmap]
rs13081675	1.00[JPT][hapmap]
rs13081694	1.00[JPT][hapmap]
rs13083670	1.00[ASN][1000 genomes]
rs13096232	1.00[ASN][1000 genomes]
rs13096256	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13097755	1.00[JPT][hapmap]
rs13100865	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs13709	1.00[JPT][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[JPT][hapmap]
rs17813772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1969356	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	1.00[JPT][hapmap]
rs2201166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272515	1.00[JPT][hapmap]
rs2319670	0.80[EUR][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs34134493	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35587339	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964791	0.87[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4146300	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4676698	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4676703	1.00[JPT][hapmap]
rs4676764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4676765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676768	1.00[ASN][1000 genomes]
rs4676776	0.82[ASW][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4676777	1.00[ASN][1000 genomes]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs4676782	1.00[JPT][hapmap]
rs4676783	1.00[JPT][hapmap]
rs4676811	1.00[JPT][hapmap]
rs6438575	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66815350	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767463	1.00[ASN][1000 genomes]
rs6768951	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6771116	0.81[EUR][1000 genomes]
rs6776878	1.00[JPT][hapmap]
rs6792814	1.00[JPT][hapmap]
rs71327229	1.00[ASN][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9880550	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6803846	RABL3	cis	cerebellum	SCAN
rs6803846	CD80	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120029400	Weak transcription	NHEK	skin
2	chr3:120024400-120032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:120024600-120032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
6	chr3:120026600-120030600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:120026800-120030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:120026800-120032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:120026800-120032600	Weak transcription	Pancreas	Pancrea
12	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
14	chr3:120027800-120030800	Weak transcription	Fetal Stomach	stomach
15	chr3:120028200-120031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:120028600-120028800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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