Variant report

Variant	rs1473696
Chromosome Location	chr1:210397552-210397553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10863816	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119444	0.85[EUR][1000 genomes]
rs12239420	0.91[EUR][1000 genomes]
rs1338298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473813	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2473814	0.86[EUR][1000 genomes]
rs2487903	0.88[ASN][1000 genomes]
rs2494183	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2494184	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2494185	0.94[EUR][1000 genomes]
rs2494186	0.95[EUR][1000 genomes]
rs4844981	0.94[EUR][1000 genomes]
rs677520	0.95[EUR][1000 genomes]
rs71571933	0.89[ASN][1000 genomes]
rs7534368	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910109	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910110	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9429839	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9430037	0.95[EUR][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473696	IRF6	cis	cerebellum	SCAN
rs1473696	SYT14	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210396000-210397600	Enhancers	Fetal Kidney	kidney
2	chr1:210397000-210397600	Enhancers	Rectal Mucosa Donor 29	rectum
3	chr1:210397200-210400600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:210397200-210400800	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:210397200-210405000	Weak transcription	Stomach Smooth Muscle	stomach

Quick Search:

Input of quick search could be:

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

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