Variant report

Variant	rs733880
Chromosome Location	chr12:75976164-75976165
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	chr12:75976057..75978739-chr12:76422916..76424954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10748283	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748284	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10785195	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785199	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10785200	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879929	0.81[EUR][1000 genomes]
rs10879930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879932	0.80[EUR][1000 genomes]
rs10879933	0.82[EUR][1000 genomes]
rs10879934	0.80[EUR][1000 genomes]
rs10879935	0.81[EUR][1000 genomes]
rs10879936	0.83[CEU][hapmap]
rs10879937	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10879943	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10879945	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs10879947	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11180575	0.82[EUR][1000 genomes]
rs11180584	0.81[EUR][1000 genomes]
rs11180601	0.84[ASN][1000 genomes]
rs11495681	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310185	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1466464	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1480005	0.95[EUR][1000 genomes]
rs1697759	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17115238	0.82[CEU][hapmap]
rs2366988	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2366989	0.89[CEU][hapmap]
rs3847671	0.80[EUR][1000 genomes]
rs3898937	0.81[EUR][1000 genomes]
rs4323912	0.83[EUR][1000 genomes]
rs4882601	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4882602	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4882631	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4882639	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4882640	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7137366	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs7300994	0.82[EUR][1000 genomes]
rs7314220	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs733881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955264	0.81[EUR][1000 genomes]
rs7956799	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958075	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7958760	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7980645	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7980713	0.81[EUR][1000 genomes]
rs899659	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9634253	0.85[CEU][hapmap]

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	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
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs733880	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs733880	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs733880	RP11-585P4.5	cis	Thyroid	GTEx
rs733880	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs733880	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs733880	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs733880	GLIPR1L2	cis	Thyroid	GTEx
rs733880	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs733880	GLIPR1L2	cis	Artery Tibial	GTEx
rs733880	GLIPR1L2	cis	lung	GTEx
rs733880	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs733880	GLIPR1L2	cis	Nerve Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75965400-75977200	Weak transcription	Fetal Brain Female	brain
2	chr12:75967000-75978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:75973600-75978800	Weak transcription	A549	lung
4	chr12:75973600-75979600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:75973800-75976400	Weak transcription	HepG2	liver
6	chr12:75974800-75977600	Enhancers	Fetal Lung	lung
7	chr12:75976000-75978400	Weak transcription	NHDF-Ad	bronchial
8	chr12:75976000-75978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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