Variant report

Variant	rs3766654
Chromosome Location	chr1:171249094-171249095
allele	A/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	SPI1	chr1:171248905-171249100	GM12891	blood:	n/a	chr1:171249059-171249072 chr1:171249023-171249032 chr1:171249022-171249035 chr1:171249021-171249034
2	SPI1	chr1:171248830-171249188	HL-60	blood:	n/a	chr1:171249022-171249035 chr1:171249021-171249034 chr1:171249023-171249032 chr1:171249059-171249072
3	SPI1	chr1:171248757-171249282	HL-60	blood:	n/a	chr1:171249022-171249035 chr1:171249021-171249034 chr1:171249023-171249032 chr1:171249059-171249072

Variant related genes	Relation type
FMO1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10912698	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10912718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912745	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912756	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038209	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12040753	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12044884	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12049309	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12118836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124080	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12127128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864258	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs16864339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2076320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421804	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72714180	0.87[AFR][1000 genomes]
rs72714189	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs732005	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7877	0.89[JPT][hapmap];0.81[ASN][1000 genomes]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3766654	FMO1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171237800-171255200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:171238600-171253600	Weak transcription	Ovary	ovary
3	chr1:171241600-171255200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:171244800-171250000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:171246800-171249200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:171247600-171249800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:171248000-171250200	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:171248600-171249200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:171248600-171249400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:171249000-171250000	Enhancers	Fetal Lung	lung
11	chr1:171249000-171251000	Enhancers	Primary B cells from cord blood	blood
12	chr1:171249000-171252200	Strong transcription	Fetal Intestine Large	intestine
13	chr1:171249000-171255200	Weak transcription	Primary hematopoietic stem cells	blood

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