Variant report

Variant	rs4682502
Chromosome Location	chr3:113559111-113559112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11706726	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631130	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13088638	0.83[ASN][1000 genomes]
rs2163388	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2399490	0.86[ASN][1000 genomes]
rs2399491	0.86[ASN][1000 genomes]
rs2632257	0.80[ASN][1000 genomes]
rs2712334	0.84[ASN][1000 genomes]
rs2712366	0.86[ASN][1000 genomes]
rs4339084	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682503	0.83[ASN][1000 genomes]
rs4682504	0.83[ASN][1000 genomes]
rs4682505	0.83[ASN][1000 genomes]
rs4682506	0.83[ASN][1000 genomes]
rs62265385	0.86[ASN][1000 genomes]
rs62265402	0.82[ASN][1000 genomes]
rs736360	0.84[ASN][1000 genomes]
rs7628746	0.84[ASN][1000 genomes]
rs7636168	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv432478	chr3:113492402-113614489	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv460822	chr3:113543081-113600970	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv591302	chr3:113543081-113600970	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4682502	GRAMD1C	Cis_1M	lymphoblastoid	RTeQTL
rs4682502	GRAMD1C	cis	Esophagus Muscularis	GTEx
rs4682502	GRAMD1C	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113558200-113559200	Weak transcription	Placenta	Placenta
2	chr3:113558200-113570800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:113558400-113559400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:113558400-113566400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:113558600-113563800	Weak transcription	Liver	Liver
6	chr3:113558600-113566600	Weak transcription	Fetal Kidney	kidney
7	chr3:113558600-113566600	Weak transcription	NHLF	lung
8	chr3:113558600-113574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:113558800-113559400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:113558800-113566600	Weak transcription	HUVEC	blood vessel

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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