Variant report

Variant	rs13172746
Chromosome Location	chr5:1983710-1983711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10037957	0.81[CEU][hapmap]
rs10038119	0.98[ASN][1000 genomes]
rs10038712	0.81[CEU][hapmap]
rs10040072	0.98[ASN][1000 genomes]
rs10040620	0.81[CEU][hapmap]
rs13153232	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13189295	0.83[ASN][1000 genomes]
rs13359574	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16902267	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17518774	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872775	0.98[ASN][1000 genomes]
rs1872776	0.98[ASN][1000 genomes]
rs2035613	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2087142	0.98[ASN][1000 genomes]
rs2101404	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2352992	0.95[ASN][1000 genomes]
rs4975778	0.93[GIH][hapmap]
rs4975783	0.98[ASN][1000 genomes]
rs4975784	0.98[ASN][1000 genomes]
rs62338667	0.81[ASN][1000 genomes]
rs62338675	0.88[ASN][1000 genomes]
rs6884415	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6894003	0.98[ASN][1000 genomes]
rs9332456	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13172746	IRX4	cis	cerebellum	SCAN
rs13172746	LOC25845	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1977200-1997000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:1983600-1983800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:1983600-1984200	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:1983600-1984400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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