Variant report

Variant	rs13138986
Chromosome Location	chr4:152719310-152719311
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	NFYB	chr4:152718975-152719514	GM12878	blood:	n/a	chr4:152719212-152719227
2	NFYA	chr4:152719122-152719337	GM12878	blood:	n/a	n/a
3	NFYB	chr4:152719088-152719332	Hela-S3	cervix:	n/a	chr4:152719212-152719227
4	NFYB	chr4:152719053-152719435	K562	blood:	n/a	chr4:152719212-152719227

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152718279..152720566-chr4:152730426..152732102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249184	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10007015	0.83[EUR][1000 genomes]
rs10007167	0.83[EUR][1000 genomes]
rs10019048	0.83[EUR][1000 genomes]
rs10023298	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028410	0.85[EUR][1000 genomes]
rs10028961	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10049728	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10049991	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10776524	0.82[EUR][1000 genomes]
rs1105534	0.83[EUR][1000 genomes]
rs1105535	0.83[EUR][1000 genomes]
rs1105536	0.83[EUR][1000 genomes]
rs11734799	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932383	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331037	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502055	0.83[EUR][1000 genomes]
rs13137669	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13146981	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355413	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1366909	0.83[EUR][1000 genomes]
rs1511170	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17027798	0.81[EUR][1000 genomes]
rs17360475	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864300	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877187	0.82[EUR][1000 genomes]
rs1896883	0.81[EUR][1000 genomes]
rs2007218	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2007445	0.83[EUR][1000 genomes]
rs2303866	0.91[EUR][1000 genomes]
rs2840130	0.83[EUR][1000 genomes]
rs28637056	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28710456	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749561	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3749563	0.81[EUR][1000 genomes]
rs3792691	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4383600	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4571	0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs4643789	0.82[AMR][1000 genomes]
rs4696104	0.83[EUR][1000 genomes]
rs4696109	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696111	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696283	0.81[EUR][1000 genomes]
rs4696284	0.83[EUR][1000 genomes]
rs4696285	0.83[EUR][1000 genomes]
rs4696291	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696294	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535809	0.83[EUR][1000 genomes]
rs6535811	0.83[EUR][1000 genomes]
rs6535812	0.83[EUR][1000 genomes]
rs6535813	0.81[EUR][1000 genomes]
rs6535814	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6535815	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6535817	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535818	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6535819	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535821	0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810860	0.83[EUR][1000 genomes]
rs6817058	0.83[EUR][1000 genomes]
rs6817586	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6818667	0.82[EUR][1000 genomes]
rs6823002	0.82[EUR][1000 genomes]
rs6823194	0.82[EUR][1000 genomes]
rs6823421	0.83[EUR][1000 genomes]
rs6823423	0.83[EUR][1000 genomes]
rs6823462	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832562	0.83[EUR][1000 genomes]
rs6833368	0.83[EUR][1000 genomes]
rs6834095	0.83[EUR][1000 genomes]
rs6838966	0.83[EUR][1000 genomes]
rs6839074	0.83[EUR][1000 genomes]
rs6840360	0.82[EUR][1000 genomes]
rs6840678	0.82[EUR][1000 genomes]
rs6841204	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs6841783	0.83[EUR][1000 genomes]
rs6845944	0.82[EUR][1000 genomes]
rs6846114	0.82[EUR][1000 genomes]
rs6849050	0.83[EUR][1000 genomes]
rs7439465	0.81[EUR][1000 genomes]
rs749982	0.83[EUR][1000 genomes]
rs751012	0.83[EUR][1000 genomes]
rs751014	0.83[EUR][1000 genomes]
rs7663045	0.96[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667197	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669977	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671651	0.81[EUR][1000 genomes]
rs7684350	0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907237	0.83[EUR][1000 genomes]
rs9307887	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9998462	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13138986	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152711000-152720000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:152712600-152720200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:152717200-152721200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:152717400-152721600	Enhancers	Stomach Mucosa	stomach
5	chr4:152717600-152721200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr4:152717600-152722000	Enhancers	Duodenum Mucosa	Duodenum
7	chr4:152717600-152722400	Enhancers	Fetal Intestine Large	intestine
8	chr4:152717600-152722400	Enhancers	Fetal Intestine Small	intestine
9	chr4:152717600-152723200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:152717800-152719400	Enhancers	Liver	Liver
11	chr4:152718000-152719400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:152718400-152719400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:152718600-152720800	Weak transcription	NHEK	skin
14	chr4:152718800-152719600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:152719200-152719400	Flanking Active TSS	Fetal Heart	heart
16	chr4:152719200-152720600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:152719200-152727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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