Variant report

Variant	rs10069929
Chromosome Location	chr5:60040060-60040061
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60017651..60020271-chr5:60037416..60040413,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10039303	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10043291	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10050803	1.00[CEU][hapmap]
rs10054744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057004	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10058456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10440618	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471493	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939860	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs10939862	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1117674	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1117675	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117676	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1117677	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740327	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs11741754	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs11948543	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap]
rs11954496	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11955398	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs11959922	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12186391	0.83[ASN][1000 genomes]
rs12514253	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs12515025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs12517174	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12517207	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12522801	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12651791	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12655977	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379114	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs1379115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1379116	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1444237	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1456742	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1456743	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1460958	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17387940	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1824120	0.81[ASN][1000 genomes]
rs1870014	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs1960479	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2061250	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs2085409	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2085410	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2085411	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085413	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2100584	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2409792	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs2409794	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs286154	0.82[CHB][hapmap]
rs286158	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2898288	0.94[ASN][1000 genomes]
rs3857236	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs3899221	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4398599	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400080	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406099	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4447941	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4527549	0.96[ASN][1000 genomes]
rs4577661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700384	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700387	0.82[EUR][1000 genomes]
rs4700388	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55854817	0.82[ASN][1000 genomes]
rs6449490	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449491	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6882727	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887434	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887637	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755077	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7701708	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7707698	0.83[ASN][1000 genomes]
rs7709056	0.91[ASN][1000 genomes]
rs7720233	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs7730342	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs897672	0.84[CEU][hapmap]
rs930864	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9654363	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686489	0.83[ASN][1000 genomes]
rs9942410	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv968917	chr5:60039988-60040709	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10069929	ELOVL7	cis	parietal	SCAN
rs10069929	ERCC8	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60036200-60044800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60037400-60047600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:60039200-60040200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:60039600-60041000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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