Variant report

Variant	rs4323912
Chromosome Location	chr12:75955371-75955372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75946731..75948885-chr12:75954512..75956708,2	MCF-7	breast:
2	chr12:75955365..75957575-chr12:75958658..75961087,2	K562	blood:
3	chr12:75953057..75955882-chr12:76429674..76432038,2	MCF-7	breast:
4	chr12:75953077..75955881-chr12:76035661..76037808,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10748282	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785195	0.82[EUR][1000 genomes]
rs10785198	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10879929	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879930	0.82[EUR][1000 genomes]
rs10879932	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879933	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879934	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879935	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879936	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879938	0.89[CEU][hapmap]
rs10879945	0.81[CEU][hapmap]
rs11180562	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180575	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180584	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180598	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11180603	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11514051	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11519910	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11520226	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12811250	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1697759	0.81[EUR][1000 genomes]
rs17115238	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054518	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366989	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886826	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34406885	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3847671	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3898937	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4882631	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882635	0.80[ASN][1000 genomes]
rs58886425	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60465677	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6582293	0.87[EUR][1000 genomes]
rs7137610	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7300994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305673	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7314220	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315474	0.81[ASN][1000 genomes]
rs733880	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs733881	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7955264	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956673	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7956799	0.81[EUR][1000 genomes]
rs7956953	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7958508	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962144	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7962276	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7979460	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979600	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7980713	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634253	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4323912	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs4323912	GLIPR1L2	cis	Artery Tibial	GTEx
rs4323912	GLIPR1L2	cis	Thyroid	GTEx
rs4323912	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4323912	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs4323912	RP11-585P4.5	cis	Artery Tibial	GTEx
rs4323912	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4323912	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs4323912	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs4323912	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs4323912	GLIPR1L2	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75946600-75957600	Weak transcription	Fetal Brain Male	brain
2	chr12:75948000-75958200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:75948800-75958200	Weak transcription	Osteobl	bone
4	chr12:75950800-75959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:75953800-75959000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:75954200-75955400	Weak transcription	Pancreas	Pancrea
7	chr12:75954400-75956200	Weak transcription	Fetal Lung	lung
8	chr12:75954400-75956800	Weak transcription	Fetal Brain Female	brain
9	chr12:75954600-75956600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:75954600-75957200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:75954600-75964800	Weak transcription	Brain Substantia Nigra	brain
12	chr12:75954800-75957200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:75954800-75958200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:75954800-75958200	Weak transcription	HMEC	breast
15	chr12:75955000-75958200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:75955200-75955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:75955200-75956200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:75955200-75957200	Weak transcription	Esophagus	oesophagus
19	chr12:75955200-75957200	Weak transcription	NHDF-Ad	bronchial
20	chr12:75955200-75957400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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