Variant report

Variant	rs12040753
Chromosome Location	chr1:171232213-171232214
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10912698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912718	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10912745	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10912756	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12022278	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12022340	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12044884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118836	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12124080	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12127128	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12954	0.84[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16864258	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076320	1.00[ASW][hapmap];0.83[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2421804	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766654	0.83[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72714180	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72714189	0.90[EUR][1000 genomes]
rs732005	0.91[AFR][1000 genomes];0.90[EUR][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
rs12040753	FMO1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171228200-171232600	Weak transcription	Placenta	Placenta
2	chr1:171228200-171232600	Weak transcription	Fetal Stomach	stomach
3	chr1:171228400-171233000	Strong transcription	Fetal Intestine Large	intestine
4	chr1:171228600-171232400	Weak transcription	Fetal Lung	lung
5	chr1:171228600-171232800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:171228600-171233000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:171228600-171235200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:171228800-171233000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:171228800-171244400	Weak transcription	Fetal Kidney	kidney
10	chr1:171229200-171232400	Weak transcription	Ovary	ovary
11	chr1:171229200-171234600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:171229400-171235000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:171230600-171235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:171230600-171236200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:171230800-171232400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:171232000-171232400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:171232200-171234200	Strong transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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