Variant report

Variant	rs12148532
Chromosome Location	chr15:73929859-73929860
allele	C/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	MAFF	chr15:73929724-73930155	HepG2	liver:	n/a	chr15:73929949-73929967
2	FOS	chr15:73929460-73930220	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr15:73929489-73930266	MCF10A-Er-Src	breast:	n/a	chr15:73929671-73929682
4	STAT3	chr15:73929463-73930248	MCF10A-Er-Src	breast:	n/a	chr15:73929671-73929682
5	STAT3	chr15:73929491-73930265	MCF10A-Er-Src	breast:	n/a	chr15:73929671-73929682
6	MAFK	chr15:73929742-73930132	HepG2	liver:	n/a	chr15:73929951-73929966
7	CTCF	chr15:73928345-73931106	A549	lung:	n/a	chr15:73928992-73929005 chr15:73928985-73929006 chr15:73928991-73929007 chr15:73928990-73929008 chr15:73928996-73929005 chr15:73928992-73929005 chr15:73928993-73929003
8	STAT3	chr15:73929495-73930262	MCF10A-Er-Src	breast:	n/a	chr15:73929671-73929682
9	MAFK	chr15:73929785-73930128	IMR90	lung:	n/a	chr15:73929951-73929966
10	MAFK	chr15:73929692-73930140	HepG2	liver:	n/a	chr15:73929951-73929966
11	FOS	chr15:73929433-73930227	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr15:73928826-73930148	MCF10A-Er-Src	breast:	n/a	n/a
13	MAFF	chr15:73929754-73929997	K562	blood:	n/a	chr15:73929949-73929967

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73921937..73932817-chr15:73973872..73983627,19	MCF-7	breast:
2	chr15:73928891..73929975-chr15:73969289..73970101,4	K562	blood:

Variant related genes	Relation type
NPTN	TF binding region
ENSG00000103855	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11072428	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072429	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072430	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs12148719	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12185108	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12593246	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594595	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1383616	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1481089	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16958079	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17185294	0.82[TSI][hapmap]
rs3743500	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495069	0.86[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7169374	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176654	0.83[MEX][hapmap]
rs8023823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028089	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036954	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs8037836	0.86[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs899981	0.87[TSI][hapmap]
rs9920359	0.82[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12148532	TLE3	cis	parietal	SCAN
rs12148532	ARIH1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73926600-73930000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:73926600-73930000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:73926600-73931400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:73926800-73930400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:73927000-73931600	Weak transcription	Placenta	Placenta
6	chr15:73927400-73932200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:73928600-73930400	Enhancers	Fetal Intestine Large	intestine
8	chr15:73928600-73931400	Enhancers	GM12878-XiMat	blood
9	chr15:73928800-73930400	Enhancers	NHEK	skin
10	chr15:73928800-73930800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:73929000-73930000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:73929000-73930200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:73929000-73930400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:73929000-73930400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr15:73929200-73930200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr15:73929200-73930200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:73929200-73930200	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr15:73929200-73930400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:73929200-73930400	Enhancers	HMEC	breast
20	chr15:73929600-73930200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:73929600-73930200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:73929800-73940000	Weak transcription	Placenta Amnion	Placenta Amnion

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