Variant report

Variant	rs17350523
Chromosome Location	chr1:171217445-171217446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10157270	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489230	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798240	0.87[ASN][1000 genomes]
rs10798252	0.91[ASN][1000 genomes]
rs10798253	0.94[ASN][1000 genomes]
rs10798263	0.95[JPT][hapmap]
rs10912475	0.87[ASN][1000 genomes]
rs10912529	0.94[ASN][1000 genomes]
rs10912537	0.95[JPT][hapmap]
rs10912542	0.95[ASN][1000 genomes]
rs10912552	0.95[JPT][hapmap]
rs11806072	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12069067	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12078953	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12080576	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090485	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133385	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12405613	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12566823	0.95[JPT][hapmap]
rs12567956	0.92[ASN][1000 genomes]
rs12730305	0.94[ASN][1000 genomes]
rs13353034	0.85[YRI][hapmap]
rs16864245	0.85[YRI][hapmap]
rs1989656	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008706	0.87[ASN][1000 genomes]
rs2020862	0.95[JPT][hapmap]
rs2049922	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064078	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075987	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2075990	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2075991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179105	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2205723	0.95[ASN][1000 genomes]
rs2205724	0.95[JPT][hapmap]
rs2205727	0.98[ASN][1000 genomes]
rs2205728	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2205729	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223228	0.94[ASN][1000 genomes]
rs2223232	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2421709	0.91[ASN][1000 genomes]
rs2421710	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421711	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35152982	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738813	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3754494	0.88[ASN][1000 genomes]
rs3754495	0.95[JPT][hapmap]
rs3768569	0.95[JPT][hapmap]
rs3768570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4480395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916182	0.95[ASN][1000 genomes]
rs4916191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916192	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425394	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425413	0.99[ASN][1000 genomes]
rs6657314	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6672029	0.97[ASN][1000 genomes]
rs6692260	0.95[ASN][1000 genomes]
rs6692347	0.95[JPT][hapmap]
rs6699803	0.95[ASN][1000 genomes]
rs6701076	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703439	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513485	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524635	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525342	0.87[ASN][1000 genomes]
rs7529080	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531713	0.95[ASN][1000 genomes]
rs7531971	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7536822	0.99[ASN][1000 genomes]
rs7538013	0.93[ASN][1000 genomes]
rs7545923	0.87[ASN][1000 genomes]
rs7553869	0.97[ASN][1000 genomes]
rs7887505	0.83[ASN][1000 genomes]
rs926268	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17350523	FMO2	cis	cerebellum	SCAN
rs17350523	RP1-127D3.4	cis	Artery Tibial	GTEx
rs17350523	FMO3	cis	cerebellum	SCAN
rs17350523	DUSP27	cis	parietal	SCAN
rs17350523	FMO2	cis	Artery Tibial	GTEx
rs17350523	TIPRL	cis	parietal	SCAN
rs17350523	FMO2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171200800-171220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:171211400-171218400	Weak transcription	Fetal Lung	lung
3	chr1:171215800-171220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:171216000-171220000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:171216400-171217600	Enhancers	Fetal Intestine Large	intestine
6	chr1:171216600-171217600	Enhancers	Fetal Intestine Small	intestine
7	chr1:171217000-171220200	Weak transcription	Pancreas	Pancrea
8	chr1:171217200-171220400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:171217200-171220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:171217400-171217600	Enhancers	Liver	Liver

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