Variant report

Variant	rs732686
Chromosome Location	chr3:111803780-111803781
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	RCOR1	chr3:111803561-111804066	K562	blood:	n/a	n/a
2	GATA3	chr3:111803642-111804329	MCF-7	breast:	n/a	n/a
3	FOSL2	chr3:111803762-111804211	HepG2	liver:	n/a	chr3:111803996-111804005 chr3:111803995-111804004 chr3:111803995-111804006
4	KAP1	chr3:111803774-111804516	U2OS	brain:	n/a	chr3:111803994-111804003
5	JUND	chr3:111803755-111804076	K562	blood:	n/a	chr3:111803996-111804005 chr3:111803994-111804005 chr3:111803995-111804004
6	SP1	chr3:111803770-111804237	A549	lung:	n/a	n/a
7	FOSL2	chr3:111803705-111804306	A549	lung:	n/a	chr3:111803996-111804005 chr3:111803995-111804004 chr3:111803995-111804006

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111803332..111805315-chr3:112279253..112281220,2	MCF-7	breast:
2	chr3:111799117..111801268-chr3:111802175..111804910,2	MCF-7	breast:

Variant related genes	Relation type
C3orf52	TF binding region
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10511304	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10511310	1.00[CHB][hapmap]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[ASN][1000 genomes]
rs10934164	1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11926389	1.00[CHB][hapmap]
rs12489470	1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12636943	1.00[CHB][hapmap]
rs13063452	1.00[CHB][hapmap]
rs13064242	1.00[CHB][hapmap]
rs1388858	1.00[CHB][hapmap]
rs1388859	1.00[CHB][hapmap]
rs1492479	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1492489	1.00[CHB][hapmap]
rs17444215	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs17446282	1.00[CHB][hapmap]
rs28370976	1.00[ASN][1000 genomes]
rs4234409	1.00[CHB][hapmap]
rs4234411	1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	1.00[CHB][hapmap]
rs4434123	1.00[CHB][hapmap]
rs4538347	1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	1.00[CHB][hapmap]
rs4682393	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs56062310	0.88[AMR][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62280198	0.88[AMR][1000 genomes]
rs62280199	0.88[AMR][1000 genomes]
rs6781844	1.00[CHB][hapmap]
rs6787323	1.00[CHB][hapmap]
rs6789875	1.00[CHB][hapmap]
rs6797177	1.00[CHB][hapmap]
rs6801795	1.00[CHB][hapmap]
rs6804836	1.00[CHB][hapmap]
rs6805112	1.00[CHB][hapmap]
rs6805397	1.00[CHB][hapmap]
rs73216052	1.00[ASN][1000 genomes]
rs73223638	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7615460	1.00[CHB][hapmap]
rs7621431	1.00[ASN][1000 genomes]
rs7625249	1.00[CHB][hapmap]
rs7631673	1.00[ASN][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7637682	1.00[CHB][hapmap]
rs9288939	1.00[CHB][hapmap]
rs9288942	1.00[CHB][hapmap]
rs9810170	1.00[CHB][hapmap]
rs9811691	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9818025	1.00[ASN][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9855755	1.00[ASN][1000 genomes]
rs9862316	1.00[ASN][1000 genomes]
rs9868226	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]

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	esv2755927	chr3:111794310-111834310	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs732686	GCET2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111794800-111804800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:111795200-111804200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111795200-111804800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:111799600-111804400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:111801800-111804600	Enhancers	Fetal Heart	heart
6	chr3:111802000-111804200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:111802200-111804600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:111802800-111804400	Enhancers	Fetal Intestine Small	intestine
9	chr3:111802800-111804600	Enhancers	Fetal Intestine Large	intestine
10	chr3:111803000-111804000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:111803000-111804400	Enhancers	Primary T cells from cord blood	blood
12	chr3:111803000-111804400	Enhancers	Fetal Thymus	thymus
13	chr3:111803000-111804600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:111803200-111804000	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:111803200-111804400	Enhancers	Stomach Mucosa	stomach
16	chr3:111803400-111804000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:111803400-111804400	Enhancers	Thymus	Thymus
18	chr3:111803400-111804600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:111803400-111804600	Enhancers	A549	lung
20	chr3:111803400-111804800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr3:111803600-111803800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:111803600-111804400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
23	chr3:111803600-111804600	Enhancers	K562	blood
24	chr3:111803600-111804800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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