Variant report

Variant	rs11830640
Chromosome Location	chr12:75956915-75956916
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	chr12:75955678..75958303-chr12:75962611..75964917,2	MCF-7	breast:
2	chr12:75955365..75957575-chr12:75958658..75961087,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11180560	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1147995	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1147997	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610328	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12811160	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12822493	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12827986	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1290026	0.94[ASN][1000 genomes]
rs1383100	0.91[ASN][1000 genomes]
rs17220228	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1824981	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2054517	0.94[ASN][1000 genomes]
rs2700521	0.94[ASN][1000 genomes]
rs34170388	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35708464	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3847672	0.94[ASN][1000 genomes]
rs3847673	0.94[ASN][1000 genomes]
rs56049502	0.94[ASN][1000 genomes]
rs56222143	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933387	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11830640	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 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	chr12:75954600-75957200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:75954600-75964800	Weak transcription	Brain Substantia Nigra	brain
8	chr12:75954800-75957200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:75954800-75958200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:75954800-75958200	Weak transcription	HMEC	breast
11	chr12:75955000-75958200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:75955200-75957200	Weak transcription	Esophagus	oesophagus
13	chr12:75955200-75957200	Weak transcription	NHDF-Ad	bronchial
14	chr12:75955200-75957400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:75955800-75958200	Weak transcription	Spleen	Spleen
16	chr12:75956400-75961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:75956600-75957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:75956600-75958200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:75956800-75957000	Active TSS	Fetal Brain Female	brain

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