Variant report

Variant	rs11059472
Chromosome Location	chr12:122665017-122665018
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	NFIC	chr12:122665007-122665711	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:122664973-122665583	HUVEC	blood vessel:	n/a	n/a
4	FOSL2	chr12:122665007-122665698	SK-N-SH	brain:	n/a	n/a
5	EP300	chr12:122664967-122665591	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr12:122664923-122665908	IMR90	lung:	n/a	n/a
7	TCF12	chr12:122664988-122665770	SK-N-SH	brain:	n/a	n/a
8	CEBPB	chr12:122664544-122665666	IMR90	lung:	n/a	chr12:122664676-122664687

Variant related genes	Relation type
LRRC43	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10847516	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058789	0.86[ASN][1000 genomes]
rs11059505	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11059675	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608363	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11613060	0.82[ASN][1000 genomes]
rs12816786	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828783	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4040811	0.87[ASN][1000 genomes]
rs4372487	0.87[ASN][1000 genomes]
rs6489217	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305669	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953139	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955910	0.86[ASN][1000 genomes]
rs7968808	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972875	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11059472	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr12:122663000-122665200	Weak transcription	HepG2	liver
8	chr12:122664600-122665400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:122664600-122665400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:122664600-122665400	Enhancers	NH-A	brain
11	chr12:122664600-122665800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:122664600-122665800	Enhancers	HUVEC	blood vessel
13	chr12:122665000-122665400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:122665000-122665400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:122665000-122665400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:122665000-122665400	Enhancers	HSMMtube	muscle
17	chr12:122665000-122665400	Enhancers	NHLF	lung
18	chr12:122665000-122665400	Enhancers	Osteobl	bone
19	chr12:122665000-122665600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:122665000-122665800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:122665000-122665800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:122665000-122665800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:122665000-122665800	Enhancers	HMEC	breast
24	chr12:122665000-122665800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links