Variant report

Variant	rs1464552
Chromosome Location	chr8:104359873-104359874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104352324..104354992-chr8:104357088..104360934,4	MCF-7	breast:
2	chr8:104357721..104360271-chr8:104361773..104363841,2	MCF-7	breast:
3	chr8:104353548..104356424-chr8:104358804..104361378,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1004468	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10505042	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1053917	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1095713	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1095714	0.87[ASN][1000 genomes]
rs11781252	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11987172	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12164188	0.94[ASN][1000 genomes]
rs12546491	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12550097	0.92[ASN][1000 genomes]
rs1357354	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1370008	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1370009	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1464550	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522708	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1522710	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1522711	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1522712	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs16870346	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1851483	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1916117	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010308	0.97[ASN][1000 genomes]
rs2388532	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2642363	0.87[ASN][1000 genomes]
rs2642364	0.87[ASN][1000 genomes]
rs2642366	0.87[ASN][1000 genomes]
rs2642368	0.87[ASN][1000 genomes]
rs2687351	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28392906	0.88[ASN][1000 genomes]
rs2917550	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934719	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2948447	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3104033	0.82[GIH][hapmap]
rs3133827	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3133837	0.82[GIH][hapmap]
rs35019987	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35935697	0.91[ASN][1000 genomes]
rs3736047	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3808553	1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs3808554	1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs3808556	0.92[ASN][1000 genomes]
rs3808559	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4734698	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62525511	0.92[ASN][1000 genomes]
rs7008838	0.85[ASN][1000 genomes]
rs7012843	0.94[ASN][1000 genomes]
rs827530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs827534	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs827535	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs827536	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs827541	0.82[GIH][hapmap]
rs827547	0.81[EUR][1000 genomes]
rs827550	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827552	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827554	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827579	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs827580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs827583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827584	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs827585	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs827586	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865461	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs865462	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1023181	chr8:104298542-104366365	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1016395	chr8:104327541-104473005	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1464552	FZD6	cis	cerebellum	SCAN
rs1464552	SLC25A32	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104328200-104361200	Weak transcription	Pancreas	Pancrea
2	chr8:104342400-104360000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:104351800-104360200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:104355000-104363200	Enhancers	NHLF	lung
5	chr8:104355200-104361200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:104355600-104360600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr8:104355600-104361000	Enhancers	NH-A	brain
8	chr8:104355600-104362000	Enhancers	Osteobl	bone
9	chr8:104355600-104362600	Enhancers	NHDF-Ad	bronchial
10	chr8:104355800-104363800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:104356000-104361200	Weak transcription	Gastric	stomach
12	chr8:104356800-104360000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:104357200-104360200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:104357200-104360200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:104357400-104361200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr8:104357600-104361000	Enhancers	HSMM	muscle
17	chr8:104357800-104360400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:104357800-104361000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr8:104357800-104361200	Weak transcription	Placenta	Placenta
20	chr8:104357800-104383400	Weak transcription	Aorta	Aorta
21	chr8:104358000-104361400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:104358400-104360000	Weak transcription	HSMMtube	muscle
23	chr8:104358800-104361800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:104359000-104360400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:104359000-104363800	Enhancers	Fetal Heart	heart
26	chr8:104359200-104361200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr8:104359200-104362800	Enhancers	Fetal Stomach	stomach
28	chr8:104359400-104360400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:104359600-104361000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:104359600-104361000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:104359600-104361600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:104359600-104362000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:104359800-104361600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:104359800-104361800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:104359800-104362000	Enhancers	HUVEC	blood vessel

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