Variant report

Variant	rs11059505
Chromosome Location	chr12:122665285-122665286
allele	C/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	PBX3	chr12:122665002-122665586	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr12:122665231-122665427	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr12:122665232-122665527	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr12:122665007-122665711	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr12:122665065-122665560	SK-N-SH	brain:	n/a	n/a
6	EP300	chr12:122665188-122665514	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr12:122664973-122665583	HUVEC	blood vessel:	n/a	n/a
8	FOS	chr12:122665256-122665455	MCF10A-Er-Src	breast:	n/a	chr12:122665414-122665425
9	FOSL2	chr12:122665007-122665698	SK-N-SH	brain:	n/a	n/a
10	EP300	chr12:122664967-122665591	SK-N-SH	brain:	n/a	n/a
11	JUN	chr12:122665103-122665564	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:122665061-122665501	HUVEC	blood vessel:	n/a	n/a
13	RCOR1	chr12:122664923-122665908	IMR90	lung:	n/a	n/a
14	TCF12	chr12:122664988-122665770	SK-N-SH	brain:	n/a	n/a
15	JUND	chr12:122665089-122665591	SK-N-SH	brain:	n/a	n/a
16	FOS	chr12:122665164-122665610	MCF10A-Er-Src	breast:	n/a	chr12:122665414-122665425
17	MAFK	chr12:122665241-122665616	IMR90	lung:	n/a	n/a
18	POLR2A	chr12:122665050-122665619	HUVEC	blood vessel:	n/a	n/a
19	FOS	chr12:122665195-122665611	MCF10A-Er-Src	breast:	n/a	chr12:122665414-122665425
20	POLR2A	chr12:122665242-122665412	SK-N-SH	brain:	n/a	n/a
21	PBX3	chr12:122665060-122665570	SK-N-SH	brain:	n/a	n/a
22	TCF12	chr12:122665055-122665714	SK-N-SH	brain:	n/a	n/a
23	EP300	chr12:122665191-122665542	SK-N-SH_RA	brain:	n/a	n/a
24	FOS	chr12:122665256-122665513	MCF10A-Er-Src	breast:	n/a	chr12:122665414-122665425
25	MYC	chr12:122665266-122665457	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:122665191-122665575	SK-N-SH	brain:	n/a	n/a
27	STAT3	chr12:122665270-122665446	MCF10A-Er-Src	breast:	n/a	n/a
28	GATA3	chr12:122665042-122665742	SK-N-SH	brain:	n/a	n/a
29	FOS	chr12:122665054-122665641	HUVEC	blood vessel:	n/a	chr12:122665414-122665425
30	GATA2	chr12:122665078-122665576	HUVEC	blood vessel:	n/a	n/a
31	CEBPB	chr12:122664544-122665666	IMR90	lung:	n/a	chr12:122664676-122664687

Variant related genes	Relation type
LRRC43	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1047796	0.87[MEX][hapmap]
rs1047813	0.87[MEX][hapmap]
rs10744335	0.91[MEX][hapmap]
rs10847516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11058789	0.88[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11059094	0.91[MEX][hapmap]
rs11059472	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11059675	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11608363	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12816786	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461580	0.91[MEX][hapmap]
rs28605425	0.91[MEX][hapmap]
rs28652632	0.91[MEX][hapmap]
rs4040811	0.84[ASN][1000 genomes]
rs4372487	0.88[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4758685	0.87[MEX][hapmap]
rs4758690	0.91[MEX][hapmap]
rs6489217	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489244	0.87[MEX][hapmap]
rs7305669	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485447	0.91[MEX][hapmap]
rs7487608	0.91[MEX][hapmap]
rs7953139	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7955910	0.82[ASN][1000 genomes]
rs7968808	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972875	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972979	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11059505	GPR81	cis	cerebellum	SCAN
rs11059505	P2RX4	cis	parietal	SCAN
rs11059505	PSMD9	cis	cerebellum	SCAN
rs11059505	FAM101A	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122658600-122667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122658800-122667400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:122662200-122667200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:122662400-122667200	Weak transcription	Liver	Liver
5	chr12:122662400-122667200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:122662400-122667200	Weak transcription	Fetal Intestine Small	intestine
7	chr12:122664600-122665400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:122664600-122665400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:122664600-122665400	Enhancers	NH-A	brain
10	chr12:122664600-122665800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:122664600-122665800	Enhancers	HUVEC	blood vessel
12	chr12:122665000-122665400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:122665000-122665400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:122665000-122665400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:122665000-122665400	Enhancers	HSMMtube	muscle
16	chr12:122665000-122665400	Enhancers	NHLF	lung
17	chr12:122665000-122665400	Enhancers	Osteobl	bone
18	chr12:122665000-122665600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:122665000-122665800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:122665000-122665800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:122665000-122665800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:122665000-122665800	Enhancers	HMEC	breast
23	chr12:122665000-122665800	Enhancers	NHEK	skin
24	chr12:122665200-122665400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:122665200-122665400	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:122665200-122665400	Enhancers	Right Ventricle	heart
27	chr12:122665200-122665400	Enhancers	HepG2	liver

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