Variant report

Variant	rs6660102
Chromosome Location	chr1:159211064-159211065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11265156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069029	0.81[AMR][1000 genomes]
rs12072644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34217855	0.95[EUR][1000 genomes]
rs3845625	0.82[CEU][hapmap]
rs61828190	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61828203	0.99[EUR][1000 genomes]
rs61828208	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61828210	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61828211	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61828213	0.94[EUR][1000 genomes]
rs6656286	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72711391	0.99[EUR][1000 genomes]
rs72713603	0.97[EUR][1000 genomes]
rs7549785	0.88[MEX][hapmap]

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	nsv872487	chr1:159196765-159342439	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv946448	chr1:159209579-159211067	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6660102	B4GALT3	cis	parietal	SCAN
rs6660102	DUSP23	cis	parietal	SCAN
rs6660102	POU5F1P4	cis	cerebellum	SCAN
rs6660102	KIRREL	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159199600-159211800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:159210200-159217000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	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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