Variant report

Variant	rs679625
Chromosome Location	chr11:58648231-58648232
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	chr11:58648139-58648384	HepG2	liver:	n/a	chr11:58648287-58648300
2	EP300	chr11:58648032-58648406	HepG2	liver:	n/a	n/a
3	FOXA1	chr11:58648036-58648475	HepG2	liver:	n/a	n/a
4	CEBPB	chr11:58648024-58648392	HepG2	liver:	n/a	chr11:58648287-58648300
5	FOXA1	chr11:58647976-58648544	HepG2	liver:	n/a	n/a
6	HNF4A	chr11:58648110-58648399	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339
7	MYC	chr11:58648181-58648368	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr11:58648183-58648434	A549	lung:	n/a	chr11:58648287-58648300
9	FOXA1	chr11:58647950-58648372	HepG2	liver:	n/a	n/a
10	FOXA1	chr11:58648027-58648516	HepG2	liver:	n/a	n/a
11	TEAD4	chr11:58648024-58648594	HepG2	liver:	n/a	n/a
12	FOXA2	chr11:58647992-58648393	HepG2	liver:	n/a	n/a
13	HNF4G	chr11:58648037-58648391	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338
14	HDAC2	chr11:58648138-58648463	HepG2	liver:	n/a	n/a
15	HDAC2	chr11:58648041-58648453	HepG2	liver:	n/a	n/a
16	ARID3A	chr11:58648155-58648546	HepG2	liver:	n/a	n/a
17	JUND	chr11:58648146-58648342	HepG2	liver:	n/a	n/a
18	EP300	chr11:58648140-58648429	HepG2	liver:	n/a	n/a
19	HNF4A	chr11:58648083-58648385	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339
20	CEBPB	chr11:58648118-58648482	HepG2	liver:	n/a	chr11:58648287-58648300
21	RCOR1	chr11:58648138-58648400	HepG2	liver:	n/a	n/a
22	JUN	chr11:58648179-58648402	HepG2	liver:	n/a	n/a
23	GATA3	chr11:58648189-58648326	SH-SY5Y	brain:	n/a	n/a
24	SP1	chr11:58648000-58648522	HepG2	liver:	n/a	n/a
25	HNF4G	chr11:58648088-58648436	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338
26	CEBPB	chr11:58648074-58648804	HepG2	liver:	n/a	chr11:58648287-58648300
27	EP300	chr11:58648078-58648464	HepG2	liver:	n/a	n/a
28	FOXA2	chr11:58647895-58648633	HepG2	liver:	n/a	n/a
29	MYBL2	chr11:58647971-58648550	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GLYATL1P2	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792184	0.84[CEU][hapmap]
rs10792185	0.84[CEU][hapmap]
rs10896825	0.84[CEU][hapmap]
rs10896854	0.83[CEU][hapmap]
rs10896856	0.84[CEU][hapmap]
rs10896857	0.84[CEU][hapmap]
rs10896858	0.84[CEU][hapmap]
rs10896859	0.84[CEU][hapmap]
rs11229651	0.84[CEU][hapmap]
rs11229655	0.84[CEU][hapmap]
rs11229656	0.84[CEU][hapmap]
rs11229658	0.84[CEU][hapmap]
rs12225778	0.84[CEU][hapmap]
rs12799196	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17153009	0.83[CEU][hapmap]
rs1938698	0.84[CEU][hapmap]
rs1938701	0.87[CEU][hapmap]
rs1938714	0.83[CEU][hapmap]
rs1943280	0.84[CEU][hapmap]
rs1943281	0.83[CEU][hapmap]
rs1943282	0.84[CEU][hapmap]
rs2156346	0.84[CEU][hapmap]
rs2849855	0.85[ASN][1000 genomes]
rs473287	0.84[CEU][hapmap]
rs483101	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs488093	0.82[ASN][1000 genomes]
rs4939226	0.84[CEU][hapmap]
rs4939229	0.84[CEU][hapmap]
rs4939230	0.84[CEU][hapmap]
rs4939231	0.84[CEU][hapmap]
rs497118	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507224	0.84[CEU][hapmap]
rs533438	0.85[ASN][1000 genomes]
rs550272	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558274	0.88[CEU][hapmap]
rs570146	0.84[CEU][hapmap]
rs572006	0.84[CEU][hapmap]
rs596847	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs599275	0.85[ASN][1000 genomes]
rs608043	0.83[ASN][1000 genomes]
rs615781	0.85[ASN][1000 genomes]
rs620633	0.82[ASN][1000 genomes]
rs644238	0.85[ASN][1000 genomes]
rs645667	0.85[ASN][1000 genomes]
rs658309	0.85[ASN][1000 genomes]
rs667445	0.84[CEU][hapmap]
rs678727	0.85[ASN][1000 genomes]
rs7933339	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1048605	chr11:58534660-58672438	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1045858	chr11:58547772-58674568	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1052173	chr11:58553516-58678496	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv508634	chr11:58624088-58657382	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1824025	chr11:58626835-58669877	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1831269	chr11:58626835-58669877	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv528475	chr11:58632368-58656808	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1831555	chr11:58632395-58653147	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs679625	GPR44	cis	parietal	SCAN
rs679625	C11orf31	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58635000-58668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:58645600-58652400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:58647600-58649000	Enhancers	Liver	Liver
4	chr11:58647600-58649000	Enhancers	HepG2	liver
5	chr11:58648000-58654400	Weak transcription	Fetal Lung	lung
6	chr11:58648000-58655000	Weak transcription	Fetal Intestine Small	intestine

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