Variant report

Variant	rs1488266
Chromosome Location	chr3:112164278-112164279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1072896	0.93[ASN][1000 genomes]
rs1473485	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1488265	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859561	0.90[ASN][1000 genomes]
rs16859563	0.90[ASN][1000 genomes]
rs16859568	0.90[ASN][1000 genomes]
rs16859570	0.90[ASN][1000 genomes]
rs16859573	0.90[ASN][1000 genomes]
rs16859587	0.93[ASN][1000 genomes]
rs2633577	0.83[EUR][1000 genomes]
rs2683893	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2683906	0.83[EUR][1000 genomes]
rs2683907	0.84[EUR][1000 genomes]
rs2683908	0.84[EUR][1000 genomes]
rs2705537	0.81[EUR][1000 genomes]
rs2705538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112269	0.83[EUR][1000 genomes]
rs56713746	0.93[ASN][1000 genomes]
rs56735831	0.90[ASN][1000 genomes]
rs56830153	0.83[ASN][1000 genomes]
rs57048961	0.90[ASN][1000 genomes]
rs57240433	0.90[ASN][1000 genomes]
rs58144611	0.90[ASN][1000 genomes]
rs58164505	0.90[ASN][1000 genomes]
rs58315065	0.90[ASN][1000 genomes]
rs58441702	0.90[ASN][1000 genomes]
rs58953251	0.93[ASN][1000 genomes]
rs59191788	0.90[ASN][1000 genomes]
rs59429955	0.90[ASN][1000 genomes]
rs59650289	0.90[ASN][1000 genomes]
rs59925989	0.90[ASN][1000 genomes]
rs60001227	0.80[ASN][1000 genomes]
rs60044977	0.93[ASN][1000 genomes]
rs60202763	0.90[ASN][1000 genomes]
rs60340975	0.90[ASN][1000 genomes]
rs60413363	0.93[ASN][1000 genomes]
rs60733172	0.90[ASN][1000 genomes]
rs60819545	0.90[ASN][1000 genomes]
rs60882964	0.93[ASN][1000 genomes]
rs61147417	0.90[ASN][1000 genomes]
rs61446034	0.90[ASN][1000 genomes]
rs72936241	0.90[ASN][1000 genomes]
rs72936252	0.90[ASN][1000 genomes]
rs72936259	0.90[ASN][1000 genomes]
rs72936271	0.93[ASN][1000 genomes]
rs924310	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953716	0.90[ASN][1000 genomes]
rs963541	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1488266	BOC	cis	cerebellum	SCAN
rs1488266	ATG3	cis	cerebellum	SCAN
rs1488266	ATG3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112157600-112165200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:112157800-112165200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:112161200-112167400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:112163000-112166800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:112163800-112166000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:112164000-112165000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:112164000-112165200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:112164000-112165600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:112164000-112166000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:112164000-112168400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:112164200-112165600	Enhancers	HSMM	muscle
12	chr3:112164200-112165800	Enhancers	HSMMtube	muscle

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