Variant report

Variant	rs1340754
Chromosome Location	chr1:70168012-70168013
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1340758	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1340773	0.94[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1884580	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60968692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6687106	0.91[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010921	chr1:70148694-70182578	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv998121	chr1:70154234-70182578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1340754	C1orf141	cis	cerebellum	SCAN
rs1340754	SRSF11	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70162000-70168800	Weak transcription	Fetal Brain Female	brain
2	chr1:70163200-70171200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:70167800-70168200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:70167800-70168400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:70167800-70168400	Enhancers	HMEC	breast
6	chr1:70167800-70168600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:70167800-70168600	Enhancers	NHEK	skin

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