Variant report

Variant	rs1109162
Chromosome Location	chr11:76891661-76891662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10466706	0.87[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10466707	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793239	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899355	0.85[AFR][1000 genomes]
rs10899356	1.00[CEU][hapmap];0.95[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]
rs10899357	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899358	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899359	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899360	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1109163	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109977	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11237106	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237109	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237110	0.81[EUR][1000 genomes]
rs11237118	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11237119	0.81[EUR][1000 genomes]
rs11237121	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12421897	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12577334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577724	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12792197	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12802853	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12806868	0.81[EUR][1000 genomes]
rs1944034	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076968	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2077198	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2155179	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2186659	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276283	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276285	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276286	0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276287	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276288	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2276294	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3740762	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781690	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3781691	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs3781694	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3781695	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944148	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945155	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945157	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4945158	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4945159	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4945160	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs7117606	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7122023	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7481443	0.81[EUR][1000 genomes]
rs7932992	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7933106	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7942355	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7943136	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7947922	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7952285	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs867505	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs867507	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs867508	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs948958	0.87[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs948963	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs948968	0.83[CEU][hapmap]
rs948970	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816632	chr11:76751285-76927014	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1109162	RNF169	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76880400-76916600	Weak transcription	Right Atrium	heart
2	chr11:76883800-76898400	Weak transcription	Colonic Mucosa	Colon
3	chr11:76885200-76896000	Strong transcription	Fetal Intestine Large	intestine
4	chr11:76885400-76896000	Strong transcription	Fetal Intestine Small	intestine
5	chr11:76886000-76894600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:76887000-76895000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:76887600-76902600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:76887800-76894000	Weak transcription	Brain Anterior Caudate	brain
9	chr11:76887800-76899600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:76887800-76902800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:76888200-76893400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr11:76888200-76894000	Strong transcription	Spleen	Spleen
13	chr11:76888600-76896000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:76889200-76894600	Strong transcription	Pancreas	Pancrea
15	chr11:76890000-76891800	Enhancers	Fetal Muscle Leg	muscle
16	chr11:76890000-76892400	Enhancers	Fetal Muscle Trunk	muscle
17	chr11:76890200-76892200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr11:76890600-76893400	Weak transcription	Right Ventricle	heart
19	chr11:76890800-76892400	Weak transcription	Gastric	stomach
20	chr11:76890800-76893000	Strong transcription	Fetal Stomach	stomach
21	chr11:76890800-76918400	Weak transcription	Ovary	ovary
22	chr11:76891000-76891800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:76891000-76894200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:76891200-76902800	Weak transcription	Adipose Nuclei	Adipose
25	chr11:76891400-76894800	Strong transcription	Placenta	Placenta
26	chr11:76891400-76899200	Strong transcription	Liver	Liver
27	chr11:76891600-76891800	Enhancers	Brain Hippocampus Middle	brain
28	chr11:76891600-76893000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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