Variant report

Variant	rs11180455
Chromosome Location	chr12:75695442-75695443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:75695255-75695655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75694427..75696955-chr12:75721959..75724062,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257823	TF binding region
ENSG00000180881	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10506668	0.81[MEX][hapmap]
rs10879900	0.81[CEU][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes]
rs10879922	0.81[MEX][hapmap]
rs11180428	0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs11180435	0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs11180441	0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs11180456	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11180458	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11180465	0.82[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs11180470	0.81[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs11180473	0.81[JPT][hapmap];0.90[AFR][1000 genomes]
rs11180540	0.86[MEX][hapmap]
rs11180548	0.81[MEX][hapmap]
rs11610111	0.80[ASN][1000 genomes]
rs11610112	0.80[ASN][1000 genomes]
rs11615934	0.89[AMR][1000 genomes]
rs12366348	0.81[JPT][hapmap]
rs12369556	0.81[MEX][hapmap]
rs12372516	0.81[JPT][hapmap]
rs12581394	0.82[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes]
rs12581416	0.86[MEX][hapmap]
rs1909979	0.86[MEX][hapmap]
rs3087687	0.86[MEX][hapmap]
rs4394867	0.81[MEX][hapmap]
rs4565940	0.81[MEX][hapmap]
rs4623941	0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs4882618	0.86[MEX][hapmap]
rs4882687	0.82[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs4882689	0.81[JPT][hapmap]
rs60971359	0.80[AMR][1000 genomes]
rs6582285	0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7136911	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs7297994	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs7298343	0.89[MEX][hapmap]
rs7302219	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7485576	0.82[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954879	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs7969930	0.86[MEX][hapmap]
rs7974011	0.85[MEX][hapmap]
rs7975661	0.82[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs7978312	0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv520424	chr12:75646788-75740883	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv526556	chr12:75653281-75740883	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv899309	chr12:75664655-75712662	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv899310	chr12:75682796-75707396	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv899311	chr12:75692261-75712662	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11180455	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs11180455	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs11180455	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs11180455	GLIPR1L2	cis	Artery Tibial	GTEx
rs11180455	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs11180455	RP11-585P4.5	cis	Artery Tibial	GTEx
rs11180455	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs11180455	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs11180455	GLIPR1L2	cis	cerebellum	SCAN
rs11180455	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs11180455	GLIPR1L2	cis	lung	GTEx
rs11180455	GLIPR1L2	cis	Nerve Tibial	GTEx
rs11180455	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11180455	GLIPR1L2	cis	parietal	SCAN
rs11180455	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs11180455	GLIPR1L2	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75679600-75699200	Weak transcription	Aorta	Aorta
2	chr12:75681200-75711400	Weak transcription	Psoas Muscle	Psoas
3	chr12:75682200-75699200	Weak transcription	Right Ventricle	heart
4	chr12:75682600-75699200	Weak transcription	Left Ventricle	heart
5	chr12:75683400-75697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:75689800-75697200	Weak transcription	Adipose Nuclei	Adipose
7	chr12:75690200-75699400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:75690600-75697200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:75691000-75699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:75691600-75697200	Weak transcription	Brain Anterior Caudate	brain
11	chr12:75691800-75699400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:75692400-75699200	Weak transcription	Ovary	ovary
13	chr12:75695000-75696800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:75695200-75697600	Weak transcription	Liver	Liver
15	chr12:75695400-75699200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links