Variant report

Variant	rs39342
Chromosome Location	chr7:103462575-103462576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs153960	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs155220	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262334	0.84[TSI][hapmap]
rs262341	1.00[CHB][hapmap]
rs262342	0.82[TSI][hapmap]
rs3819491	0.82[TSI][hapmap]
rs39332	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs39336	0.83[CEU][hapmap];0.88[AMR][1000 genomes]
rs39337	0.83[CEU][hapmap];0.88[AMR][1000 genomes]
rs39338	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39339	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39341	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39346	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745541	1.00[CHB][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1843940	chr7:103421702-103590285	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv523031	chr7:103457789-103470499	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3431631	chr7:103462366-103464364	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv934055	chr7:103462527-103473944	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs39342	PMS2L1	cis	parietal	SCAN
rs39342	CNPY4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103457800-103472000	Weak transcription	HepG2	liver
2	chr7:103461200-103482400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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