Variant report

Variant	rs624273
Chromosome Location	chr11:65712413-65712414
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	CEBPB	chr11:65712346-65712635	HepG2	liver:	n/a	chr11:65712512-65712523
2	FOXA1	chr11:65712282-65712629	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:65712382-65712604	HepG2	liver:	n/a	chr11:65712512-65712523

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65686026..65690385-chr11:65711034..65716101,7	MCF-7	breast:
2	chr11:65625517..65628088-chr11:65710841..65713644,2	MCF-7	breast:

Variant related genes	Relation type
TSGA10IP	TF binding region
ENSG00000175573	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1151505	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1151512	0.81[EUR][1000 genomes]
rs1151523	0.83[CHD][hapmap];0.83[GIH][hapmap]
rs1192168	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1204649	0.83[EUR][1000 genomes]
rs12361552	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12792888	0.80[EUR][1000 genomes]
rs12797319	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1308733	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786175	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs3016868	0.81[EUR][1000 genomes]
rs470192	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs491973	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs493899	0.83[EUR][1000 genomes]
rs501353	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs503524	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs528736	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs531612	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs538954	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs542332	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs550435	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs552130	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs556643	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs559078	0.82[EUR][1000 genomes]
rs55928757	0.84[EUR][1000 genomes]
rs590318	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs593525	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs606978	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs613924	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs617791	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs61893932	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs632578	0.85[CEU][hapmap]
rs634534	0.81[CEU][hapmap]
rs637571	0.81[GIH][hapmap]
rs642293	0.88[EUR][1000 genomes]
rs655744	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs660118	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs669371	0.86[CHD][hapmap];0.85[GIH][hapmap]
rs679581	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs688862	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs694156	0.80[AMR][1000 genomes]
rs7105628	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
6	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
9	esv3444925	chr11:65687425-65714023	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs624273	EFEMP2	cis	cerebellum	SCAN
rs624273	EIF1AD	cis	parietal	SCAN
rs624273	RAB1B	cis	cerebellum	SCAN
rs624273	SNX32	cis	parietal	SCAN
rs624273	TSGA10IP	cis	cerebellum	SCAN
rs624273	PACS1	cis	parietal	SCAN
rs624273	LRRN4CL	cis	cerebellum	SCAN
rs624273	BANF1	Cis_1M	lymphoblastoid	RTeQTL
rs624273	FADS3	cis	parietal	SCAN
rs624273	SNX32	cis	cerebellum	SCAN
rs624273	BANF1	cis	multi-tissue	Pritchard
rs624273	ZNF408	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65688800-65715000	Weak transcription	Right Atrium	heart
2	chr11:65699800-65712600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:65700000-65712600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:65705600-65712800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:65705800-65712800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:65709200-65712800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:65709200-65726000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:65709400-65712800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:65709400-65712800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:65709400-65713200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:65709400-65717800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:65710200-65712800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:65710400-65713400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:65711600-65712600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:65712200-65712600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:65712200-65712600	Flanking Active TSS	HepG2	liver
17	chr11:65712200-65712800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:65712400-65712600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:65712400-65712800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:65712400-65712800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr11:65712400-65712800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr11:65712400-65713200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr11:65712400-65716400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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