Variant report

Variant	rs17217158
Chromosome Location	chr12:75871264-75871265
allele	A/G
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	BCL11A	chr12:75871011-75871291	GM12878	blood:	n/a	n/a
2	EBF1	chr12:75871029-75871264	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GLIPR1	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10506667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506669	0.90[ASN][1000 genomes]
rs11180480	0.83[JPT][hapmap]
rs11180499	0.90[ASN][1000 genomes]
rs11180552	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11180560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11355	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11609405	0.93[ASN][1000 genomes]
rs11609538	0.87[ASN][1000 genomes]
rs11610328	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11611121	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611609	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]
rs11612665	0.96[ASN][1000 genomes]
rs11829975	0.90[ASN][1000 genomes]
rs12423560	0.90[ASN][1000 genomes]
rs12423750	0.90[ASN][1000 genomes]
rs12424262	0.87[ASN][1000 genomes]
rs12425122	0.97[ASN][1000 genomes]
rs12580524	0.90[ASN][1000 genomes]
rs12811160	0.82[EUR][1000 genomes]
rs12812559	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]
rs12815116	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12817746	0.90[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12821144	0.90[ASN][1000 genomes]
rs12822366	0.96[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12822505	0.96[ASN][1000 genomes]
rs12826635	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12827668	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12833944	0.90[ASN][1000 genomes]
rs1501634	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs15513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552039	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1604381	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17818307	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1824981	0.86[EUR][1000 genomes]
rs1909977	0.87[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2134140	0.87[ASN][1000 genomes]
rs2202105	0.96[ASN][1000 genomes]
rs2279244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs2306391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs34508642	0.96[ASN][1000 genomes]
rs35124104	0.97[ASN][1000 genomes]
rs35244242	0.96[ASN][1000 genomes]
rs35351465	0.96[ASN][1000 genomes]
rs35619460	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36113316	0.90[ASN][1000 genomes]
rs3741495	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[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]
rs3809118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809121	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4019356	0.90[ASN][1000 genomes]
rs4420306	0.96[ASN][1000 genomes]
rs4760596	0.96[ASN][1000 genomes]
rs4882626	0.90[ASN][1000 genomes]
rs61933361	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61933362	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961005	0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17217158	GLIPR1	cis	lesional skin	skin_eQTL
rs17217158	KRR1	cis	Muscle Skeletal	GTEx
rs17217158	GLIPR1	cis	normal skin	skin_eQTL
rs17217158	GLIPR1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75865400-75874800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:75866600-75871800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:75866600-75873400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:75868400-75874400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:75868400-75875600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:75868600-75873000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:75868600-75874000	Weak transcription	NHEK	skin
8	chr12:75868600-75874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:75868800-75872000	Weak transcription	HMEC	breast
10	chr12:75868800-75873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:75869800-75871800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:75869800-75871800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:75870000-75871600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr12:75870000-75871800	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:75870000-75872000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:75870200-75872600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:75870400-75872000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:75870400-75872000	Enhancers	Dnd41	blood
19	chr12:75870600-75872000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:75870600-75873600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:75870600-75874000	Enhancers	Primary T cells from cord blood	blood
22	chr12:75870800-75873000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:75870800-75873600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:75870800-75873600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:75870800-75873800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:75871000-75871400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:75871000-75871800	Enhancers	Primary B cells from cord blood	blood
28	chr12:75871000-75873800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:75871000-75873800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:75871200-75871800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:75871200-75872000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr12:75871200-75873600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links