Variant report

Variant	rs11611609
Chromosome Location	chr12:75890652-75890653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75889808..75893135-chr12:75894450..75896351,3	K562	blood:
2	chr12:75890543..75892939-chr12:75893042..75895529,2	MCF-7	breast:
3	chr12:75889727..75892026-chr12:76809238..76812157,2	K562	blood:
4	chr12:75884651..75886505-chr12:75889602..75891842,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11180480	0.83[JPT][hapmap]
rs11180552	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11612665	0.83[ASN][1000 genomes]
rs12425122	0.84[ASN][1000 genomes]
rs12811160	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12812559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815116	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12822505	0.83[ASN][1000 genomes]
rs12826635	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827986	0.81[ASN][1000 genomes]
rs1501634	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552039	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2070162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508642	0.83[ASN][1000 genomes]
rs35124104	0.84[ASN][1000 genomes]
rs35244242	0.83[ASN][1000 genomes]
rs35351465	0.83[ASN][1000 genomes]
rs35619460	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420306	0.83[ASN][1000 genomes]
rs4760596	0.83[ASN][1000 genomes]
rs56049502	0.81[ASN][1000 genomes]
rs61933361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933387	0.81[ASN][1000 genomes]
rs7961005	0.83[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	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	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
rs11611609	GLIPR1	cis	parietal	SCAN
rs11611609	GLIPR1	cis	lesional skin	skin_eQTL
rs11611609	LRRN1	trans	cerebellum	SCAN
rs11611609	GLIPR1L2	cis	cerebellum	SCAN
rs11611609	KRR1	cis	cerebellum	SCAN
rs11611609	PTPRB	cis	parietal	SCAN
rs11611609	GLIPR1	cis	normal skin	skin_eQTL
rs11611609	GLIPR1	cis	lymphoblastoid	seeQTL
rs11611609	KRR1	cis	parietal	SCAN
rs11611609	GLIPR1	cis	uninvolved skin	skin_eQTL
rs11611609	GLIPR1L2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75874800-75895000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:75875800-75892400	Weak transcription	K562	blood
4	chr12:75875800-75892600	Weak transcription	Brain Angular Gyrus	brain
5	chr12:75875800-75894400	Weak transcription	Colonic Mucosa	Colon
6	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
7	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
9	chr12:75876400-75891400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:75876400-75894400	Weak transcription	Ovary	ovary
11	chr12:75876800-75895000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:75879000-75890800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:75879200-75892400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:75879200-75894400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:75879200-75900600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:75879800-75902000	Strong transcription	Primary B cells from cord blood	blood
17	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:75881400-75892600	Weak transcription	Fetal Brain Female	brain
19	chr12:75881400-75894400	Weak transcription	Fetal Kidney	kidney
20	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:75883200-75901800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:75883400-75894800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:75883400-75902600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr12:75883600-75891600	Weak transcription	Hela-S3	cervix
25	chr12:75883600-75901800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:75883600-75902200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:75883800-75895000	Weak transcription	Right Ventricle	heart
28	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
29	chr12:75884000-75891000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:75884000-75895800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:75884000-75896600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:75884000-75899400	Strong transcription	HSMM	muscle
33	chr12:75884200-75899000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:75884200-75901200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:75884200-75901200	Strong transcription	NH-A	brain
36	chr12:75884200-75902200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:75884400-75901600	Strong transcription	NHDF-Ad	bronchial
38	chr12:75884800-75899200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:75885000-75902200	Strong transcription	HUVEC	blood vessel
40	chr12:75885000-75902400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:75885400-75894800	Weak transcription	HepG2	liver
42	chr12:75886200-75903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:75886400-75893400	Strong transcription	GM12878-XiMat	blood
44	chr12:75886400-75899400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:75886600-75891200	Weak transcription	Brain Germinal Matrix	brain
46	chr12:75886600-75894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:75886600-75901400	Strong transcription	HMEC	breast
48	chr12:75886600-75903000	Strong transcription	Fetal Thymus	thymus
49	chr12:75886800-75902000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:75887000-75891400	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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