Variant report

Variant	rs4565938
Chromosome Location	chr12:75867949-75867950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75865659..75868414-chr12:75872510..75875016,3	K562	blood:
2	chr12:75088132..75090058-chr12:75866248..75868411,2	K562	blood:

Variant related genes	Relation type
ENSG00000139278	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10450780	0.94[ASN][1000 genomes]
rs10879908	0.87[ASN][1000 genomes]
rs10879909	0.87[ASN][1000 genomes]
rs10879910	0.91[ASN][1000 genomes]
rs10879912	0.91[ASN][1000 genomes]
rs10879917	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11180481	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180491	0.87[ASN][1000 genomes]
rs11180502	0.87[ASN][1000 genomes]
rs11180503	0.89[ASN][1000 genomes]
rs12366783	0.83[ASN][1000 genomes]
rs12369849	0.87[ASN][1000 genomes]
rs1275478	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1275480	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1275481	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs12830818	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1480004	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1604382	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1679378	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697750	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697752	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1697756	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1697757	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1795744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1824980	0.88[EUR][1000 genomes]
rs1875468	0.96[ASN][1000 genomes]
rs2036387	0.96[ASN][1000 genomes]
rs2173919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704766	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2704767	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3952732	0.91[ASN][1000 genomes]
rs4019365	0.96[ASN][1000 genomes]
rs4391857	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4393363	0.85[ASN][1000 genomes]
rs4479027	0.94[ASN][1000 genomes]
rs4882621	0.87[ASN][1000 genomes]
rs4882622	0.87[ASN][1000 genomes]
rs6582290	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7135340	0.87[ASN][1000 genomes]
rs7294749	0.96[ASN][1000 genomes]
rs7295336	0.83[ASN][1000 genomes]
rs7296471	0.93[ASN][1000 genomes]
rs7300308	0.93[ASN][1000 genomes]
rs7310735	0.85[ASN][1000 genomes]
rs7966751	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971504	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4565938	GLIPR1L2	cis	Artery Tibial	GTEx
rs4565938	GLIPR1	cis	Liver	GTEx
rs4565938	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4565938	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs4565938	GLIPR1L2	cis	Thyroid	GTEx
rs4565938	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4565938	GLIPR1L2	cis	lung	GTEx
rs4565938	GLIPR1L2	cis	parietal	SCAN
rs4565938	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4565938	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4565938	GLIPR1	cis	normal skin	skin_eQTL
rs4565938	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs4565938	GLIPR1	cis	cerebellum	SCAN
rs4565938	GLIPR1L2	cis	cerebellum	SCAN
rs4565938	GLIPR1	cis	multi-tissue	Pritchard
rs4565938	RP11-585P4.5	cis	Artery Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75863400-75868800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:75864800-75868000	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:75864800-75868000	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:75865400-75874800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:75866600-75868200	Enhancers	Primary B cells from cord blood	blood
6	chr12:75866600-75868800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:75866600-75868800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:75866600-75869000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:75866600-75871800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:75866600-75873400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:75867000-75870600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:75867200-75868800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:75867600-75868600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:75867600-75868600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:75867600-75868600	Enhancers	NHEK	skin
16	chr12:75867600-75868800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:75867600-75868800	Enhancers	HMEC	breast
18	chr12:75867800-75868200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:75867800-75868200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:75867800-75868200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr12:75867800-75868400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:75867800-75868600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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