Variant report

Variant	rs3904965
Chromosome Location	chr1:85465793-85465794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10782534	0.83[ASN][1000 genomes]
rs10873669	0.83[ASN][1000 genomes]
rs10873670	0.83[ASN][1000 genomes]
rs10873672	0.88[ASN][1000 genomes]
rs10873676	0.89[ASN][1000 genomes]
rs10873677	0.89[ASN][1000 genomes]
rs11161495	0.83[ASN][1000 genomes]
rs11161496	0.83[ASN][1000 genomes]
rs11161498	0.81[ASN][1000 genomes]
rs11161499	0.81[ASN][1000 genomes]
rs11161501	0.88[ASN][1000 genomes]
rs11161502	0.88[ASN][1000 genomes]
rs11161503	0.89[ASN][1000 genomes]
rs11161504	0.89[ASN][1000 genomes]
rs11161505	0.89[ASN][1000 genomes]
rs11485283	0.83[ASN][1000 genomes]
rs11485284	0.83[ASN][1000 genomes]
rs11799517	0.84[ASN][1000 genomes]
rs11804248	0.84[ASN][1000 genomes]
rs12091131	0.83[ASN][1000 genomes]
rs12130357	0.86[ASN][1000 genomes]
rs12730688	0.83[ASN][1000 genomes]
rs12754569	0.83[ASN][1000 genomes]
rs1439130	0.84[ASN][1000 genomes]
rs2389792	0.88[ASN][1000 genomes]
rs2389793	0.88[ASN][1000 genomes]
rs2486755	0.83[ASN][1000 genomes]
rs3850430	0.94[ASN][1000 genomes]
rs3861690	0.93[ASN][1000 genomes]
rs3895846	0.94[ASN][1000 genomes]
rs486751	0.83[ASN][1000 genomes]
rs488710	0.82[ASN][1000 genomes]
rs4907017	0.83[ASN][1000 genomes]
rs4907018	0.83[ASN][1000 genomes]
rs4907118	0.89[ASN][1000 genomes]
rs495786	0.83[ASN][1000 genomes]
rs499539	0.83[ASN][1000 genomes]
rs530486	0.83[ASN][1000 genomes]
rs531423	0.83[ASN][1000 genomes]
rs589653	0.82[ASN][1000 genomes]
rs600536	0.83[ASN][1000 genomes]
rs603746	0.83[ASN][1000 genomes]
rs625045	0.82[ASN][1000 genomes]
rs631267	0.83[ASN][1000 genomes]
rs648660	0.83[ASN][1000 genomes]
rs650529	0.80[ASN][1000 genomes]
rs651916	0.83[ASN][1000 genomes]
rs6576736	0.83[ASN][1000 genomes]
rs662948	0.83[ASN][1000 genomes]
rs6677091	0.88[ASN][1000 genomes]
rs6685363	0.83[ASN][1000 genomes]
rs668860	0.82[ASN][1000 genomes]
rs6691674	0.88[ASN][1000 genomes]
rs6691970	0.88[ASN][1000 genomes]
rs6700622	0.88[ASN][1000 genomes]
rs679167	0.82[ASN][1000 genomes]
rs726708	0.93[ASN][1000 genomes]
rs7516329	0.88[ASN][1000 genomes]
rs7516610	0.89[ASN][1000 genomes]
rs7516625	0.88[ASN][1000 genomes]
rs7519134	0.92[ASN][1000 genomes]
rs7522851	0.92[ASN][1000 genomes]
rs7541684	0.83[ASN][1000 genomes]
rs7549346	0.82[ASN][1000 genomes]
rs7552445	0.86[ASN][1000 genomes]
rs7553886	0.88[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3904965	MCOLN2	cis	Thyroid	GTEx
rs3904965	MCOLN2	cis	Artery Tibial	GTEx
rs3904965	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs3904965	MCOLN3	cis	Thyroid	GTEx
rs3904965	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:85464400-85466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85464800-85466800	Active TSS	GM12878-XiMat	blood
4	chr1:85465200-85465800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:85465200-85467000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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