Variant report

Variant	rs11520223
Chromosome Location	chr12:75768869-75768870
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10879900	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180456	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180458	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180465	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180473	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180475	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610111	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11610112	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366348	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12367329	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12368429	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12369854	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372516	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12581394	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4623941	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882616	0.81[AMR][1000 genomes]
rs4882687	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4882689	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60971359	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136911	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73191008	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73364090	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364096	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954879	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7967619	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970188	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][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	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs11520223	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs11520223	GLIPR1L2	cis	Artery Tibial	GTEx
rs11520223	GLIPR1L2	cis	Stomach	GTEx
rs11520223	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs11520223	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs11520223	GLIPR1L2	cis	Thyroid	GTEx
rs11520223	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs11520223	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs11520223	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs11520223	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs11520223	GLIPR1L2	cis	Nerve Tibial	GTEx
rs11520223	GLIPR1L2	cis	Artery Aorta	GTEx
rs11520223	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs11520223	RP11-585P4.5	cis	Thyroid	GTEx
rs11520223	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs11520223	GLIPR1L2	cis	lung	GTEx
rs11520223	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs11520223	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11520223	RP11-585P4.5	cis	Artery Tibial	GTEx
rs11520223	GLIPR1L2	cis	Esophagus Mucosa	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	chr12:75749800-75771800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:75754000-75784200	Weak transcription	Right Ventricle	heart
4	chr12:75757200-75783400	Weak transcription	Ovary	ovary
5	chr12:75758200-75782600	Weak transcription	Aorta	Aorta
6	chr12:75763400-75784400	Weak transcription	Left Ventricle	heart
7	chr12:75763600-75770400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:75764200-75770600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:75765600-75770200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:75766800-75770200	Weak transcription	Spleen	Spleen
11	chr12:75767400-75772000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:75768600-75772200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:75768800-75769400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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