Variant report

Variant	rs17411879
Chromosome Location	chr1:79358211-79358212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:79356582..79358429-chr1:79361774..79364231,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10127633	0.92[ASN][1000 genomes]
rs10157100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10157101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10157118	0.94[ASN][1000 genomes]
rs10158521	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1048361	0.98[ASN][1000 genomes]
rs1061728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11162575	0.92[ASN][1000 genomes]
rs11162576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11162578	0.95[ASN][1000 genomes]
rs11162579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11162580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11162582	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11578886	0.93[ASN][1000 genomes]
rs11579537	0.90[CHB][hapmap]
rs11583810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11585250	0.94[ASN][1000 genomes]
rs11589071	0.94[ASN][1000 genomes]
rs11589307	0.95[ASN][1000 genomes]
rs11589308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12021727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12022724	0.85[ASN][1000 genomes]
rs12023385	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12023956	0.85[ASN][1000 genomes]
rs12024704	0.85[ASN][1000 genomes]
rs12026854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12028201	0.93[ASN][1000 genomes]
rs12029928	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12036315	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs12037077	0.86[AFR][1000 genomes]
rs12041776	0.94[ASN][1000 genomes]
rs12042046	0.92[ASN][1000 genomes]
rs12044660	0.85[ASN][1000 genomes]
rs12045470	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12047525	0.85[ASN][1000 genomes]
rs12047963	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12048362	0.85[ASN][1000 genomes]
rs12048990	0.87[ASN][1000 genomes]
rs12049419	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12240096	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12404123	0.95[ASN][1000 genomes]
rs12405227	0.95[ASN][1000 genomes]
rs12405579	0.92[ASN][1000 genomes]
rs12405700	0.95[ASN][1000 genomes]
rs12405826	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12406020	0.95[ASN][1000 genomes]
rs12406914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12409126	0.92[CHD][hapmap];0.95[ASN][1000 genomes]
rs1248478	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1261980	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1489383	0.86[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs1552569	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1552570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17102430	0.93[ASN][1000 genomes]
rs17102432	0.93[ASN][1000 genomes]
rs17102465	0.95[ASN][1000 genomes]
rs17102491	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17102494	0.95[ASN][1000 genomes]
rs17102512	0.94[ASN][1000 genomes]
rs17102538	0.85[ASN][1000 genomes]
rs17102541	0.85[ASN][1000 genomes]
rs17102547	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1906831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1906832	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035725	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2035727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2635120	0.99[ASN][1000 genomes]
rs2882991	0.93[ASN][1000 genomes]
rs34763897	0.93[ASN][1000 genomes]
rs3811438	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4271160	0.95[ASN][1000 genomes]
rs4376689	0.85[ASN][1000 genomes]
rs4650621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4650622	0.84[ASN][1000 genomes]
rs4650623	0.84[CHB][hapmap]
rs56828724	0.93[ASN][1000 genomes]
rs59001904	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59554507	0.93[ASN][1000 genomes]
rs6657515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6678427	0.93[ASN][1000 genomes]
rs6699540	0.85[ASN][1000 genomes]
rs7526334	0.95[ASN][1000 genomes]
rs7527803	0.86[CHB][hapmap]
rs7527882	0.82[CHB][hapmap]
rs7527890	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999624	chr1:79230028-79448222	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535013	chr1:79230028-79448222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546619	chr1:79233493-79614989	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2830430	chr1:79310760-79555593	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1010441	chr1:79320299-79555315	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1001894	chr1:79351364-79542576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv535014	chr1:79351364-79542576	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv871089	chr1:79353655-79471959	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17411879	NEXN	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79348600-79405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:79350800-79358600	Strong transcription	HUVEC	blood vessel
3	chr1:79351000-79360800	Weak transcription	Left Ventricle	heart
4	chr1:79351000-79365600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:79351000-79367600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:79357600-79358400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:79357600-79358400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:79357600-79358600	Enhancers	Osteobl	bone
9	chr1:79358000-79358400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:79358200-79358400	Flanking Active TSS	NHDF-Ad	bronchial
11	chr1:79358200-79358600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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