Variant report

Variant	rs12812559
Chromosome Location	chr12:75904102-75904103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75895269..75897744-chr12:75903455..75905180,2	MCF-7	breast:
2	chr12:75897120..75901453-chr12:75903276..75905265,4	MCF-7	breast:
3	chr12:75722764..75725346-chr12:75903212..75905334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180881	Chromatin interaction
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

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];1.00[YRI][hapmap]
rs11180480	0.83[JPT][hapmap]
rs11180552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11355	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611609	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]
rs11612665	0.83[ASN][1000 genomes]
rs12425122	0.84[ASN][1000 genomes]
rs12811160	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12815116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12822505	0.83[ASN][1000 genomes]
rs12826635	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552039	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.84[AMR][1000 genomes];0.93[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];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	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]
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	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	0.97[AMR][1000 genomes];0.99[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:7 , 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
7	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12812559	GLIPR1	cis	uninvolved skin	skin_eQTL
rs12812559	GLIPR1	cis	normal skin	skin_eQTL
rs12812559	GLIPR1	cis	lesional skin	skin_eQTL
rs12812559	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs12812559	KRR1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
2	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:75892800-75904400	Weak transcription	Gastric	stomach
4	chr12:75895400-75904200	Weak transcription	Right Ventricle	heart
5	chr12:75895400-75904400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:75895400-75904600	Weak transcription	Lung	lung
7	chr12:75895800-75904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:75897000-75904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:75897600-75904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:75897600-75904800	Weak transcription	Spleen	Spleen
11	chr12:75897800-75904600	Weak transcription	Left Ventricle	heart
12	chr12:75897800-75904800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:75900000-75904400	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:75900400-75904600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:75900800-75904400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:75900800-75904400	Weak transcription	Placenta	Placenta
17	chr12:75901800-75904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:75902600-75904400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:75903000-75904200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:75903000-75904200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:75903000-75904600	Enhancers	Small Intestine	intestine
22	chr12:75903200-75904200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:75903200-75904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:75903200-75904600	Flanking Active TSS	Dnd41	blood
25	chr12:75903200-75905000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:75903200-75906000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:75903400-75904200	Enhancers	Primary B cells from cord blood	blood
28	chr12:75903400-75904200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:75903400-75904200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:75903400-75904200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:75903400-75904200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:75903400-75904200	Enhancers	Colon Smooth Muscle	Colon
33	chr12:75903400-75904200	Enhancers	Fetal Thymus	thymus
34	chr12:75903400-75904200	Flanking Active TSS	HepG2	liver
35	chr12:75903400-75904400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:75903400-75904600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:75903400-75904600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:75903400-75906000	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr12:75903600-75904200	Enhancers	Brain Angular Gyrus	brain
40	chr12:75903600-75904200	Enhancers	Brain Hippocampus Middle	brain
41	chr12:75903600-75904200	Weak transcription	Ovary	ovary
42	chr12:75903600-75904200	Enhancers	Thymus	Thymus
43	chr12:75903600-75904400	Enhancers	Fetal Intestine Small	intestine
44	chr12:75903600-75904400	Flanking Active TSS	NHEK	skin
45	chr12:75903600-75904400	Flanking Active TSS	NHLF	lung
46	chr12:75903600-75904600	Enhancers	Primary B cells from peripheral blood	blood
47	chr12:75903600-75904600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:75903600-75904600	Enhancers	Stomach Mucosa	stomach
49	chr12:75903600-75904600	Flanking Active TSS	HUVEC	blood vessel
50	chr12:75903600-75904800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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