Variant report

Variant	rs3809118
Chromosome Location	chr12:75872256-75872257
allele	G/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	MYC	chr12:75872179-75872482	NB4	blood:	n/a	n/a
2	CEBPB	chr12:75872161-75872517	K562	blood:	n/a	chr12:75872335-75872348
3	SPI1	chr12:75872227-75872513	GM12878	blood:	n/a	n/a
4	SPI1	chr12:75872179-75872500	GM12891	blood:	n/a	n/a
5	SPI1	chr12:75872163-75872537	HL-60	blood:	n/a	n/a
6	POU2F2	chr12:75872143-75872590	GM12878	blood:	n/a	n/a
7	BHLHE40	chr12:75872161-75872508	GM12878	blood:	n/a	n/a
8	CREB1	chr12:75872138-75872528	GM12878	blood:	n/a	n/a
9	CEBPB	chr12:75872199-75872470	H1-hESC	embryonic stem cell:	n/a	chr12:75872335-75872348
10	CEBPB	chr12:75872141-75872572	MCF-7	breast:	n/a	chr12:75872335-75872348
11	CEBPB	chr12:75872166-75872529	A549	lung:	n/a	chr12:75872335-75872348
12	RUNX3	chr12:75871913-75872614	GM12878	blood:	n/a	chr12:75872347-75872364
13	MAX	chr12:75871912-75872569	NB4	blood:	n/a	n/a
14	CREB1	chr12:75871971-75872620	GM12878	blood:	n/a	n/a
15	SPI1	chr12:75872191-75872519	GM12891	blood:	n/a	n/a
16	EP300	chr12:75872054-75872546	GM12878	blood:	n/a	n/a
17	CEBPB	chr12:75872173-75872518	Hela-S3	cervix:	n/a	chr12:75872335-75872348
18	ZNF143	chr12:75872190-75872516	GM12878	blood:	n/a	chr12:75872313-75872322
19	RUNX3	chr12:75872162-75872585	GM12878	blood:	n/a	chr12:75872347-75872364
20	BCLAF1	chr12:75872174-75872615	GM12878	blood:	n/a	n/a
21	NFIC	chr12:75872012-75872594	GM12878	blood:	n/a	n/a
22	ATF2	chr12:75872051-75872561	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr12:75872191-75872531	GM12878	blood:	n/a	n/a
24	EBF1	chr12:75872169-75872497	GM12878	blood:	n/a	n/a
25	POU2F2	chr12:75872174-75872514	GM12878	blood:	n/a	n/a
26	CEBPB	chr12:75872145-75872732	IMR90	lung:	n/a	chr12:75872335-75872348
27	FOXM1	chr12:75872121-75872594	GM12878	blood:	n/a	n/a
28	CEBPB	chr12:75872177-75872575	MCF-7	breast:	n/a	chr12:75872335-75872348
29	SPI1	chr12:75872076-75872719	HL-60	blood:	n/a	chr12:75872091-75872100
30	CEBPB	chr12:75872176-75872513	HepG2	liver:	n/a	chr12:75872335-75872348

Variant related genes	Relation type
GLIPR1	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10506667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506669	0.90[ASN][1000 genomes]
rs11180480	0.84[JPT][hapmap]
rs11180499	0.90[ASN][1000 genomes]
rs11180552	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11180560	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11355	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11609405	0.93[ASN][1000 genomes]
rs11609538	0.87[ASN][1000 genomes]
rs11610328	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611609	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]
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]
rs12812559	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]
rs12815116	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12817746	0.90[ASN][1000 genomes]
rs12819511	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[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];0.85[JPT][hapmap]
rs12822505	0.96[ASN][1000 genomes]
rs12826635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12827668	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12833944	0.90[ASN][1000 genomes]
rs1501634	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs15513	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552039	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1604381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17217158	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]
rs17218895	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17818307	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1824981	0.83[EUR][1000 genomes]
rs1909977	0.87[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070162	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]
rs2134140	0.87[ASN][1000 genomes]
rs2202105	0.96[ASN][1000 genomes]
rs2279244	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]
rs2306391	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]
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	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36113316	0.90[ASN][1000 genomes]
rs3741495	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.90[AMR][1000 genomes];0.89[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	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61933362	0.93[AMR][1000 genomes];0.90[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
rs3809118	GLIPR1	cis	uninvolved skin	skin_eQTL
rs3809118	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs3809118	GLIPR1	cis	lesional skin	skin_eQTL
rs3809118	GLIPR1	cis	normal skin	skin_eQTL

Chromatin state (count:48 , 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	chr12:75866600-75873400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:75868400-75874400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:75868400-75875600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:75868600-75873000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:75868600-75874000	Weak transcription	NHEK	skin
7	chr12:75868600-75874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:75868800-75873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:75870200-75872600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:75870600-75873600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:75870600-75874000	Enhancers	Primary T cells from cord blood	blood
12	chr12:75870800-75873000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:75870800-75873600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:75870800-75873600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:75870800-75873800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:75871000-75873800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:75871000-75873800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:75871200-75873600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:75871400-75873800	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:75871600-75873400	Enhancers	Osteobl	bone
21	chr12:75871600-75873600	Weak transcription	HSMMtube	muscle
22	chr12:75871600-75874400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:75871800-75872400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:75871800-75872800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr12:75871800-75872800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:75871800-75873400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr12:75872000-75872400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:75872000-75872400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:75872000-75872400	Flanking Active TSS	NHDF-Ad	bronchial
30	chr12:75872000-75872600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:75872000-75872600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:75872000-75872600	Flanking Active TSS	Dnd41	blood
33	chr12:75872000-75872600	Flanking Active TSS	GM12878-XiMat	blood
34	chr12:75872000-75872800	Enhancers	HMEC	breast
35	chr12:75872000-75873200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr12:75872000-75873400	Enhancers	NHLF	lung
37	chr12:75872000-75873600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:75872000-75873600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:75872000-75873800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:75872000-75874000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:75872000-75874000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr12:75872000-75874200	Enhancers	Fetal Thymus	thymus
43	chr12:75872000-75874200	Enhancers	Thymus	Thymus
44	chr12:75872200-75872400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:75872200-75873200	Weak transcription	NH-A	brain
46	chr12:75872200-75873800	Enhancers	Primary hematopoietic stem cells	blood
47	chr12:75872200-75873800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr12:75872200-75874000	Enhancers	Primary monocytes fromperipheralblood	blood

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