Variant report

Variant	rs6604719
Chromosome Location	chr1:223670323-223670324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10907383	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10907386	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11261291	0.91[ASN][1000 genomes]
rs11261296	0.90[ASN][1000 genomes]
rs11586368	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12041055	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12119648	0.82[ASN][1000 genomes]
rs4072756	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233523	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4489550	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511103	0.87[ASN][1000 genomes]
rs4512641	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4661276	0.88[ASN][1000 genomes]
rs6683246	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692980	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1013538	chr1:223626487-223670776	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6604719	SUSD4	cis	cerebellum	SCAN
rs6604719	WDR26	cis	parietal	SCAN
rs6604719	ENAH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223661400-223671600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:223661400-223674000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:223667600-223673200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:223670200-223670800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:223670200-223671000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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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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