Variant report

Variant	rs6701779
Chromosome Location	chr1:85479196-85479197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10782536	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10873676	0.82[EUR][1000 genomes]
rs10873677	0.80[EUR][1000 genomes]
rs10873678	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10873679	0.81[EUR][1000 genomes]
rs10873682	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10873683	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11161502	0.82[EUR][1000 genomes]
rs11161513	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11161514	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12034421	0.81[ASN][1000 genomes]
rs12138711	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3850430	0.81[EUR][1000 genomes]
rs3895846	0.81[EUR][1000 genomes]
rs4907123	0.88[AMR][1000 genomes]
rs4907125	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6701779	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs6701779	MCOLN2	cis	Thyroid	GTEx
rs6701779	MCOLN3	cis	Thyroid	GTEx
rs6701779	MCOLN2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85478800-85483800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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