Variant report

Variant	rs7116339
Chromosome Location	chr11:102465281-102465282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11225339	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631143	1.00[JPT][hapmap]
rs1711419	0.85[JPT][hapmap]
rs1711424	1.00[JPT][hapmap]
rs1711428	1.00[JPT][hapmap]
rs1784411	1.00[JPT][hapmap]
rs1784416	0.85[JPT][hapmap]
rs61344910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72984055	0.84[ASN][1000 genomes]
rs7934692	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv1815657	chr11:102413582-102490794	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832252	chr11:102445479-102627879	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7116339	TRPC6	cis	parietal	SCAN
rs7116339	CASP1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102462200-102470000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:102463800-102466800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:102463800-102469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:102464000-102468800	Weak transcription	HUVEC	blood vessel
5	chr11:102464000-102469200	Weak transcription	NHEK	skin
6	chr11:102464000-102470800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:102464200-102469000	Weak transcription	HMEC	breast
8	chr11:102465000-102465400	Enhancers	Fetal Intestine Small	intestine
9	chr11:102465200-102465800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:102465200-102468600	Enhancers	Fetal Intestine Large	intestine

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