Variant report

Variant	rs1542570
Chromosome Location	chr12:75998603-75998604
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75992922..75995873-chr12:75997451..75999755,2	K562	blood:

Variant related genes	Relation type
ENSG00000257777	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10785197	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180576	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180577	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11180591	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180592	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147994	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12299578	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1351328	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1383098	0.83[ASN][1000 genomes]
rs1383101	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1480001	0.83[ASN][1000 genomes]
rs1480002	0.83[ASN][1000 genomes]
rs1611928	0.81[ASN][1000 genomes]
rs1627431	0.83[ASN][1000 genomes]
rs1630753	0.82[ASN][1000 genomes]
rs1679380	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697753	0.83[ASN][1000 genomes]
rs1795374	0.82[ASN][1000 genomes]
rs1795380	0.83[ASN][1000 genomes]
rs1795382	0.83[ASN][1000 genomes]
rs2620687	0.83[ASN][1000 genomes]
rs2652022	0.83[ASN][1000 genomes]
rs4882638	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs57091991	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7297463	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73185062	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7960251	0.93[EUR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1542570	GLIPR1L2	cis	parietal	SCAN
rs1542570	ATXN7L3B	cis	cerebellum	SCAN
rs1542570	GLIPR1L2	cis	cerebellum	SCAN
rs1542570	E2F7	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr12:75993000-75999600	Weak transcription	Brain Germinal Matrix	brain
4	chr12:75997800-76000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:75997800-76000000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:75997800-76000000	Weak transcription	NHDF-Ad	bronchial
7	chr12:75998200-75999800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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