Variant report

Variant	rs1701927
Chromosome Location	chr19:51408842-51408843
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1090649	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654513	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs1654554	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1654556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1701925	0.87[ASN][1000 genomes]
rs1701926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1701929	0.92[JPT][hapmap]
rs2235091	0.91[JPT][hapmap]
rs2569536	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2659107	0.82[JPT][hapmap]
rs2739496	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979451	0.91[JPT][hapmap]
rs3875143	0.91[JPT][hapmap]
rs806019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv511623	chr19:51400775-51408842	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
4	esv3322316	chr19:51404940-51410038	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	esv3373904	chr19:51405340-51409338	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1701927	NLRP7	cis	parietal	SCAN
rs1701927	ZSCAN5A	cis	parietal	SCAN
rs1701927	LENG8	cis	parietal	SCAN
rs1701927	PRPF31	cis	parietal	SCAN
rs1701927	ZNF548	cis	parietal	SCAN
rs1701927	ZNF28	cis	parietal	SCAN
rs1701927	GALP	cis	cerebellum	SCAN
rs1701927	ZNF418	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51408600-51409400	Weak transcription	GM12878-XiMat	blood

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

what's new

Quick links