Variant report

Variant	rs10865941
Chromosome Location	chr3:46508547-46508548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:46508534-46508590	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46508156..46510225-chr3:46511342..46513592,2	K562	blood:

Variant related genes	Relation type
LTF	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10514713	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10865942	0.90[JPT][hapmap]
rs11130093	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs11130094	0.96[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs11706090	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489117	0.80[EUR][1000 genomes]
rs12496623	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12638228	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402151	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1520483	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139634	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683242	0.82[JPT][hapmap]
rs55950019	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56233078	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762703	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6763280	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883739	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs883740	0.82[JPT][hapmap]
rs885485	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885486	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10865941	LTF	cis	brain	BrainEAC
rs10865941	LTF	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46504800-46509000	Enhancers	Spleen	Spleen
2	chr3:46506200-46508600	Enhancers	Pancreas	Pancrea
3	chr3:46506800-46509600	Weak transcription	Right Atrium	heart
4	chr3:46506800-46510800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:46507000-46509600	Weak transcription	Right Ventricle	heart
6	chr3:46507200-46509000	Enhancers	Adipose Nuclei	Adipose
7	chr3:46507400-46508800	Enhancers	Psoas Muscle	Psoas
8	chr3:46507400-46522400	Weak transcription	Gastric	stomach
9	chr3:46507600-46509000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:46507600-46514200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:46507800-46513400	Enhancers	Left Ventricle	heart
12	chr3:46508200-46508600	Enhancers	Primary B cells from cord blood	blood
13	chr3:46508200-46511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:46508200-46511400	Weak transcription	Lung	lung
15	chr3:46508400-46509400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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