Variant report

Variant	rs1383100
Chromosome Location	chr12:76000617-76000618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1026784	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10506667	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1147997	0.95[ASN][1000 genomes]
rs11540407	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11610328	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11611121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11830640	0.91[ASN][1000 genomes]
rs12811160	0.92[ASN][1000 genomes]
rs12812559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12819511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs12827986	0.97[ASN][1000 genomes]
rs1290026	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1501634	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs15513	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1552039	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs17217158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17220228	0.95[ASN][1000 genomes]
rs1824981	0.87[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2070162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2306391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2700521	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34170388	0.95[ASN][1000 genomes]
rs35708464	0.95[ASN][1000 genomes]
rs3741495	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3809118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3847672	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3847673	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56049502	0.94[ASN][1000 genomes]
rs56222143	0.95[ASN][1000 genomes]
rs61933387	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1383100	KRR1	cis	cerebellum	SCAN
rs1383100	KRR1	cis	parietal	SCAN
rs1383100	GLIPR1L2	cis	parietal	SCAN
rs1383100	GLIPR1L2	cis	cerebellum	SCAN
rs1383100	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs1383100	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs1383100	GLIPR1	cis	parietal	SCAN
rs1383100	GLIPR1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:75991800-76004800	Weak transcription	Aorta	Aorta
3	chr12:75999400-76001600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:75999600-76001400	Enhancers	Brain Germinal Matrix	brain
5	chr12:75999600-76001400	Enhancers	Brain Hippocampus Middle	brain
6	chr12:75999600-76001600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:75999600-76001600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:75999800-76001600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:75999800-76005000	Weak transcription	Pancreas	Pancrea
10	chr12:76000000-76001400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:76000000-76001400	Enhancers	Brain Angular Gyrus	brain
12	chr12:76000000-76001600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:76000200-76001400	Enhancers	Brain Anterior Caudate	brain
14	chr12:76000400-76000800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:76000400-76001200	Active TSS	Brain Substantia Nigra	brain

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