Variant report

Variant	rs2968824
Chromosome Location	chr2:55305064-55305065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55304969..55307023-chr2:55308110..55310726,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10179594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10196667	0.82[CEU][hapmap]
rs10205017	0.80[EUR][1000 genomes]
rs10746530	0.82[CEU][hapmap]
rs11125551	0.82[CEU][hapmap]
rs12989576	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs13002841	0.82[CEU][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs13023202	0.82[EUR][1000 genomes]
rs2580763	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs2580766	0.82[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2588520	0.82[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2919125	0.82[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2920839	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920861	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920872	0.87[ASN][1000 genomes]
rs2920881	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2920883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920890	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920898	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2968789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968792	0.84[ASN][1000 genomes]
rs2968810	0.87[ASN][1000 genomes]
rs2968812	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2968813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2968814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2968823	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968826	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968829	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2968831	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972065	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972067	0.90[ASN][1000 genomes]
rs2972069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972076	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972084	0.85[ASN][1000 genomes]
rs3099068	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545462	0.82[CEU][hapmap]
rs7559248	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968824	RTN4	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55299200-55318000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55304400-55309200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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