Variant report

Variant	rs2075991
Chromosome Location	chr1:171177273-171177274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10157270	0.95[ASN][1000 genomes]
rs10489230	0.96[ASN][1000 genomes]
rs10798240	0.91[ASN][1000 genomes]
rs10798252	0.96[ASN][1000 genomes]
rs10798253	0.99[ASN][1000 genomes]
rs10798263	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs10912475	0.91[ASN][1000 genomes]
rs10912529	0.98[ASN][1000 genomes]
rs10912537	0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10912538	0.80[ASN][1000 genomes]
rs10912542	0.99[ASN][1000 genomes]
rs10912552	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11806072	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs11810116	0.80[ASN][1000 genomes]
rs12069067	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12078953	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12080576	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12090485	0.94[ASN][1000 genomes]
rs12133385	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12405613	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12566823	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12567956	0.96[ASN][1000 genomes]
rs12730305	0.98[ASN][1000 genomes]
rs13353034	0.83[YRI][hapmap]
rs16864191	0.93[YRI][hapmap]
rs17350523	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]
rs1989656	0.96[ASN][1000 genomes]
rs2008706	0.91[ASN][1000 genomes]
rs2020862	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2020865	0.89[YRI][hapmap]
rs2049922	0.96[ASN][1000 genomes]
rs2064078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2075987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs2075990	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179105	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205723	0.99[ASN][1000 genomes]
rs2205724	0.95[JPT][hapmap]
rs2205727	0.95[ASN][1000 genomes]
rs2205728	0.96[ASN][1000 genomes]
rs2205729	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2223228	0.98[ASN][1000 genomes]
rs2223232	0.96[ASN][1000 genomes]
rs2236874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2421709	0.96[ASN][1000 genomes]
rs2421710	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421711	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35152982	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738813	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3754494	0.92[ASN][1000 genomes]
rs3754495	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs3768569	0.95[JPT][hapmap]
rs3768570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4480395	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916182	0.99[ASN][1000 genomes]
rs4916191	0.96[ASN][1000 genomes]
rs4916192	0.96[ASN][1000 genomes]
rs6425394	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6425413	0.96[ASN][1000 genomes]
rs6657314	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs6662773	0.80[ASN][1000 genomes]
rs6672029	0.94[ASN][1000 genomes]
rs6692260	0.99[ASN][1000 genomes]
rs6692347	0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6699803	0.99[ASN][1000 genomes]
rs6701076	0.94[ASN][1000 genomes]
rs6703439	0.96[ASN][1000 genomes]
rs7513485	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513579	0.80[ASN][1000 genomes]
rs7518899	0.80[ASN][1000 genomes]
rs7520777	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524635	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525342	0.91[ASN][1000 genomes]
rs7529080	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531713	0.92[ASN][1000 genomes]
rs7531971	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7536822	0.96[ASN][1000 genomes]
rs7538013	0.97[ASN][1000 genomes]
rs7545923	0.91[ASN][1000 genomes]
rs7553869	0.93[ASN][1000 genomes]
rs7887505	0.87[ASN][1000 genomes]
rs926268	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv1817255	chr1:171170733-171185865	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2075991	FMO2	cis	cerebellum	SCAN
rs2075991	FMO2	cis	parietal	SCAN
rs2075991	RP1-127D3.4	cis	Artery Tibial	GTEx
rs2075991	TIPRL	cis	parietal	SCAN
rs2075991	FMO3	cis	cerebellum	SCAN
rs2075991	DUSP27	cis	parietal	SCAN
rs2075991	FMO2	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156600-171179600	Weak transcription	NHLF	lung
2	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
3	chr1:171166000-171178000	Weak transcription	Psoas Muscle	Psoas
4	chr1:171166000-171184000	Weak transcription	Gastric	stomach
5	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
7	chr1:171171400-171179400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:171172200-171178600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:171173600-171179000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:171174200-171178600	Strong transcription	Left Ventricle	heart
11	chr1:171174400-171177400	Enhancers	Stomach Mucosa	stomach
12	chr1:171174600-171178200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:171174600-171178200	Strong transcription	Aorta	Aorta
14	chr1:171175600-171179000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:171176200-171177400	Enhancers	Fetal Intestine Small	intestine
16	chr1:171176800-171178600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:171176800-171179400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:171177000-171177400	Strong transcription	Fetal Lung	lung
19	chr1:171177200-171177800	Strong transcription	Adipose Nuclei	Adipose
20	chr1:171177200-171178600	Weak transcription	Liver	Liver
21	chr1:171177200-171178800	Weak transcription	Fetal Intestine Large	intestine

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