Variant report

Variant	rs11112370
Chromosome Location	chr12:105498813-105498814
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	KAP1	chr12:105498571-105498862	K562	blood:	n/a	n/a
2	CBX3	chr12:105498565-105498874	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105493621..105499511-chr12:105499874..105503218,6	MCF-7	breast:
2	chr12:105473909..105476084-chr12:105497876..105499540,2	K562	blood:
3	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:

Variant related genes	Relation type
KIAA1033	TF binding region
ENSG00000136051	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000257999	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1014502	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10431460	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459203	0.82[CEU][hapmap]
rs10459204	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs1057110	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1077896	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861334	0.80[CEU][hapmap]
rs10861339	0.81[CEU][hapmap]
rs10861359	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861361	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861363	0.84[CEU][hapmap]
rs1109433	0.86[EUR][1000 genomes]
rs11112369	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112372	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11112375	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11112376	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112379	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112388	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112409	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112412	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs11112415	0.89[EUR][1000 genomes]
rs11112416	1.00[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs11112421	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11112423	0.84[EUR][1000 genomes]
rs11112432	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs11831854	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs11832489	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11834277	0.83[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196845	0.84[ASW][hapmap];0.82[GIH][hapmap];0.80[YRI][hapmap]
rs12228093	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12228948	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12812433	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12815031	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12819309	0.87[EUR][1000 genomes]
rs12823614	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs12830078	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1317955	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1373552	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1444611	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1470381	0.87[EUR][1000 genomes]
rs2166143	0.87[CEU][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap]
rs2272495	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2293643	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293644	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2464176	0.81[ASN][1000 genomes]
rs28549976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34075890	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34983773	0.87[EUR][1000 genomes]
rs35462155	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35672903	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736628	0.84[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3794222	0.86[EUR][1000 genomes]
rs3794223	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes]
rs3794224	0.84[EUR][1000 genomes]
rs3794227	0.94[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs3817607	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829296	0.86[EUR][1000 genomes]
rs4964125	0.88[EUR][1000 genomes]
rs4964334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964335	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964336	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964338	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964339	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964340	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964342	0.94[EUR][1000 genomes]
rs55908437	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56693261	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73179994	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7485364	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs755604	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8015	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs881279	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs9919746	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11112370	KIAA1033	cis	cerebellum	SCAN
rs11112370	APPL2	cis	cerebellum	SCAN
rs11112370	C12orf75	cis	cerebellum	SCAN
rs11112370	TDG	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105494600-105500200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:105494800-105500000	Weak transcription	NHEK	skin
3	chr12:105494800-105500200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:105494800-105500200	Weak transcription	HMEC	breast
5	chr12:105494800-105500600	Weak transcription	NH-A	brain
6	chr12:105495000-105500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105495000-105500400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:105495000-105500400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:105495000-105500400	Weak transcription	Osteobl	bone
10	chr12:105495000-105500600	Weak transcription	NHDF-Ad	bronchial
11	chr12:105495000-105500800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:105495200-105500200	Weak transcription	A549	lung
13	chr12:105495200-105500200	Weak transcription	HepG2	liver
14	chr12:105495200-105500400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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