Variant report

Variant	rs10466706
Chromosome Location	chr11:76906621-76906622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76906503..76907469-chr11:77258976..77259541,2	K562	blood:
2	chr11:76906449..76907116-chr11:77268005..77269240,5	MCF-7	breast:
3	chr11:76906559..76907619-chr11:77259021..77259968,8	MCF-7	breast:
4	chr11:76906391..76907428-chr11:77080845..77082151,7	MCF-7	breast:
5	chr11:76906576..76907452-chr11:77259126..77259917,4	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10466707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][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];1.00[ASN][1000 genomes]
rs10793239	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10899356	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10899357	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899358	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899359	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899360	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109162	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]
rs1109163	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1109977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237106	0.88[EUR][1000 genomes]
rs11237109	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237110	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237111	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237118	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237119	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237120	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11237121	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237122	0.86[JPT][hapmap]
rs12421897	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12577334	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs12577724	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12792197	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12802853	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806868	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320702	0.86[JPT][hapmap]
rs1944034	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076968	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2077198	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2155179	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2186659	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276283	0.86[EUR][1000 genomes]
rs2276285	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276286	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276287	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276288	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276290	0.85[JPT][hapmap]
rs2276293	0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2276294	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3740762	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3781689	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781691	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781693	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781694	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3781695	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4944148	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945155	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4945157	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945158	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945160	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7117606	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7122023	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7481443	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927472	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7932992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7933106	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7942355	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7943136	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7947922	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7952285	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs867505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867508	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885442	0.86[JPT][hapmap]
rs948958	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948962	0.82[YRI][hapmap]
rs948963	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs948970	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
2	nsv897936	chr11:76900813-76935002	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv17589	chr11:76906030-76906635	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10466706	RNF169	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76880400-76916600	Weak transcription	Right Atrium	heart
2	chr11:76890800-76918400	Weak transcription	Ovary	ovary
3	chr11:76899800-76928200	Strong transcription	Liver	Liver
4	chr11:76903600-76928000	Weak transcription	Colonic Mucosa	Colon
5	chr11:76903600-76928600	Strong transcription	Fetal Intestine Small	intestine
6	chr11:76904000-76908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:76904000-76909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:76904000-76910600	Weak transcription	HepG2	liver
9	chr11:76904200-76927600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:76904600-76906800	Strong transcription	Spleen	Spleen
11	chr11:76904600-76913200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:76904600-76915600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:76904600-76927800	Strong transcription	Fetal Intestine Large	intestine
14	chr11:76905000-76907000	Strong transcription	Adipose Nuclei	Adipose
15	chr11:76905000-76909600	Weak transcription	Esophagus	oesophagus
16	chr11:76905400-76906800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:76905800-76907000	Enhancers	Fetal Muscle Trunk	muscle
18	chr11:76905800-76908000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr11:76906000-76907000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr11:76906000-76907400	Enhancers	Fetal Muscle Leg	muscle
21	chr11:76906000-76908600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:76906200-76906800	Enhancers	Psoas Muscle	Psoas
23	chr11:76906200-76907000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:76906200-76907000	Enhancers	HSMM	muscle
25	chr11:76906200-76907200	Enhancers	HSMMtube	muscle
26	chr11:76906400-76906800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:76906400-76906800	Enhancers	Fetal Brain Male	brain
28	chr11:76906400-76906800	Enhancers	Left Ventricle	heart
29	chr11:76906400-76907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:76906400-76907000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr11:76906400-76907000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr11:76906400-76908400	Enhancers	Stomach Mucosa	stomach
33	chr11:76906600-76906800	Enhancers	Duodenum Mucosa	Duodenum
34	chr11:76906600-76907000	Enhancers	Fetal Brain Female	brain
35	chr11:76906600-76907000	Enhancers	Gastric	stomach
36	chr11:76906600-76909200	Strong transcription	Placenta	Placenta
37	chr11:76906600-76909600	Weak transcription	Pancreas	Pancrea
38	chr11:76906600-76913200	Weak transcription	Fetal Stomach	stomach
39	chr11:76906600-76915600	Weak transcription	Right Ventricle	heart

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