Variant report

Variant	rs4882599
Chromosome Location	chr12:75778888-75778889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10450780	0.81[AMR][1000 genomes]
rs10785191	0.84[ASN][1000 genomes]
rs10879908	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10879909	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10879910	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10879912	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879914	0.84[ASN][1000 genomes]
rs10879917	0.84[AMR][1000 genomes]
rs10879921	0.81[ASN][1000 genomes]
rs11180481	0.88[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11180491	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180503	0.86[AMR][1000 genomes]
rs11180516	0.85[ASN][1000 genomes]
rs11180517	0.85[ASN][1000 genomes]
rs11180523	0.84[ASN][1000 genomes]
rs11180529	0.82[ASN][1000 genomes]
rs12305941	0.83[ASN][1000 genomes]
rs12369849	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12830818	0.86[AMR][1000 genomes]
rs1875468	0.87[AMR][1000 genomes]
rs2036387	0.86[AMR][1000 genomes]
rs2102134	0.82[ASN][1000 genomes]
rs3952732	0.86[AMR][1000 genomes]
rs4019365	0.86[AMR][1000 genomes]
rs4391857	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4393363	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882621	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4882622	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6582290	0.86[AMR][1000 genomes]
rs7135340	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7294749	0.86[AMR][1000 genomes]
rs7295336	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7296471	0.86[AMR][1000 genomes]
rs7300308	0.86[AMR][1000 genomes]
rs7310735	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4882599	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs4882599	GLIPR1L2	cis	Thyroid	GTEx
rs4882599	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs4882599	GLIPR1L2	cis	lung	GTEx
rs4882599	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4882599	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs4882599	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4882599	RP11-585P4.5	cis	Artery Tibial	GTEx
rs4882599	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs4882599	GLIPR1L2	cis	Artery Tibial	GTEx
rs4882599	GLIPR1L2	cis	Nerve Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75749600-75782800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75754000-75784200	Weak transcription	Right Ventricle	heart
3	chr12:75757200-75783400	Weak transcription	Ovary	ovary
4	chr12:75758200-75782600	Weak transcription	Aorta	Aorta
5	chr12:75763400-75784400	Weak transcription	Left Ventricle	heart
6	chr12:75772200-75785000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:75772400-75782400	Weak transcription	Psoas Muscle	Psoas
8	chr12:75772600-75782800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:75773600-75782800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:75774200-75782400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:75776600-75784800	Weak transcription	Gastric	stomach
12	chr12:75778800-75779000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr12:75778800-75782800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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