Variant report

Variant	rs11180605
Chromosome Location	chr12:76033717-76033718
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76031206..76033811-chr12:76047362..76050308,2	MCF-7	breast:
2	chr12:76032457..76035300-chr12:76104195..76106631,2	MCF-7	breast:
3	chr12:76032186..76035156-chr12:76036962..76040307,4	K562	blood:
4	chr12:76033638..76035156-chr12:76038536..76041322,2	K562	blood:
5	chr12:76032058..76036488-chr12:76038031..76041740,5	MCF-7	breast:
6	chr12:76032505..76035383-chr12:76043295..76046760,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10748283	0.83[ASN][1000 genomes]
rs10748284	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785199	0.86[ASN][1000 genomes]
rs10785200	0.86[ASN][1000 genomes]
rs10879937	0.83[ASN][1000 genomes]
rs10879938	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10879943	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10879944	0.93[ASN][1000 genomes]
rs10879945	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10879946	0.93[ASN][1000 genomes]
rs10879947	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10879948	0.93[ASN][1000 genomes]
rs11180600	0.82[ASN][1000 genomes]
rs11180601	0.86[ASN][1000 genomes]
rs11495681	0.83[ASN][1000 genomes]
rs12310185	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1466464	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1871548	0.89[ASN][1000 genomes]
rs34767748	0.95[ASN][1000 genomes]
rs34952545	0.95[ASN][1000 genomes]
rs4882601	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4882602	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4882637	0.93[ASN][1000 genomes]
rs4882639	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4882640	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7137366	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs733880	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs733881	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7958075	0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7958490	0.91[ASN][1000 genomes]
rs7958760	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7972231	0.90[ASN][1000 genomes]
rs7973399	0.91[ASN][1000 genomes]
rs7980645	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs899658	0.98[ASN][1000 genomes]
rs899659	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11180605	GLIPR1L2	cis	lung	GTEx
rs11180605	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs11180605	GLIPR1L2	cis	Nerve Tibial	GTEx
rs11180605	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs11180605	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs11180605	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs11180605	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs11180605	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs11180605	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs11180605	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs11180605	GLIPR1L2	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76026600-76035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:76029400-76034400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:76030000-76034200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:76030000-76034600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:76030000-76034600	Weak transcription	K562	blood
6	chr12:76030200-76034000	Weak transcription	GM12878-XiMat	blood
7	chr12:76030200-76034600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:76030200-76034600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:76030200-76034600	Weak transcription	HSMM	muscle
10	chr12:76030200-76034600	Weak transcription	HSMMtube	muscle
11	chr12:76030400-76034000	Weak transcription	A549	lung
12	chr12:76030400-76034200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:76030400-76034200	Weak transcription	Osteobl	bone
14	chr12:76030400-76034800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:76030400-76034800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:76030400-76035200	Weak transcription	NHLF	lung
17	chr12:76030600-76034200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:76030600-76034400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:76030600-76034800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:76030800-76034400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:76030800-76034600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:76031000-76034400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:76031000-76034400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:76031000-76034400	Weak transcription	NHDF-Ad	bronchial
25	chr12:76031000-76034600	Weak transcription	NH-A	brain
26	chr12:76031000-76034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:76031000-76034800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:76032000-76035800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:76032400-76036800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:76032400-76037200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:76032600-76036800	Enhancers	HMEC	breast
32	chr12:76032800-76036600	Enhancers	NHEK	skin
33	chr12:76033200-76035200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:76033200-76035600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:76033200-76035600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:76033400-76034200	Weak transcription	HepG2	liver
37	chr12:76033600-76033800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:76033600-76033800	Enhancers	Esophagus	oesophagus
39	chr12:76033600-76036400	Enhancers	Dnd41	blood

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