Variant report

Variant	rs13314357
Chromosome Location	chr3:136487559-136487560
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	chr3:136471103..136473077-chr3:136487227..136489991,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1052620	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12695649	1.00[ASN][1000 genomes]
rs13062352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs13080786	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	1.00[ASN][1000 genomes]
rs13100192	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[ASN][1000 genomes]
rs13433683	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs17365792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872239	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176269	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28641809	1.00[ASN][1000 genomes]
rs28750366	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs28811905	1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34804893	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35096613	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35198484	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35210994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36177165	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4038586	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767889	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	1.00[ASN][1000 genomes]
rs6806123	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs71310215	0.81[AMR][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs71336080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	1.00[ASN][1000 genomes]
rs73231903	1.00[ASN][1000 genomes]
rs7612425	1.00[ASN][1000 genomes]
rs9289513	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	0.93[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813691	1.00[ASN][1000 genomes]
rs9819856	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820717	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828088	1.00[ASN][1000 genomes]
rs9828976	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840500	1.00[ASN][1000 genomes]
rs9845862	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850364	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	1.00[ASN][1000 genomes]
rs9857966	1.00[ASN][1000 genomes]
rs9858560	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860879	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867325	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs9869630	1.00[ASN][1000 genomes]
rs9871184	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873536	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875770	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879531	1.00[ASN][1000 genomes]
rs9881831	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883189	0.93[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv33758	chr3:136480745-136492394	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13314357	RNF184	cis	multi-tissue	Pritchard
rs13314357	ERICH1	trans	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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