Variant report

Variant	rs13420379
Chromosome Location	chr2:187020342-187020343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187020003..187021879-chr2:187026559..187028779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226410	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10175720	0.86[JPT][hapmap]
rs10181623	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10193665	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10193729	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10195904	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1021281	0.87[AMR][1000 genomes]
rs10931222	0.86[JPT][hapmap]
rs11689385	0.86[AMR][1000 genomes]
rs12615701	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12616050	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13388196	0.86[JPT][hapmap]
rs13403118	0.83[EUR][1000 genomes]
rs13417421	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13419562	0.86[JPT][hapmap]
rs13427402	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1386519	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1487351	0.85[AMR][1000 genomes]
rs16827561	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2029234	0.85[AMR][1000 genomes]
rs2370661	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2370667	0.82[EUR][1000 genomes]
rs2370670	0.86[JPT][hapmap]
rs2370675	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28492747	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2887815	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2887819	0.82[EUR][1000 genomes]
rs3107177	0.82[EUR][1000 genomes]
rs33920466	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36093799	0.83[AMR][1000 genomes]
rs3919953	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4477870	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4591311	0.85[JPT][hapmap]
rs4637073	0.82[EUR][1000 genomes]
rs4667076	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6434159	0.87[AMR][1000 genomes]
rs6715226	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs6726048	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742402	0.84[ASN][1000 genomes]
rs72903699	0.87[ASN][1000 genomes]
rs7557226	0.87[ASN][1000 genomes]
rs7566117	0.87[AMR][1000 genomes]
rs7566161	0.87[AMR][1000 genomes]
rs7586293	0.89[AMR][1000 genomes]
rs7586724	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7599277	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7602735	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7605905	0.87[AMR][1000 genomes]
rs875161	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1002243	chr2:186692815-187150225	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv536077	chr2:186692815-187150225	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv875548	chr2:186798249-187164657	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1003369	chr2:186980675-187133740	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13420379	ITGAV	cis	cerebellum	SCAN
rs13420379	ITGAV	cis	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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