Variant report

Variant	rs2078267
Chromosome Location	chr11:64334114-64334115
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	ARID3A	chr11:64333745-64334390	HepG2	liver:	n/a	n/a
2	USF1	chr11:64334043-64334445	A549	lung:	n/a	chr11:64334237-64334248
3	JUND	chr11:64333981-64334427	HepG2	liver:	n/a	n/a
4	JUND	chr11:64333970-64334421	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUN	chr11:64333800-64334410	H1-hESC	embryonic stem cell:	n/a	chr11:64334226-64334239
6	POLR2A	chr11:64333970-64334465	HCT-116	colon:	n/a	n/a
7	RCOR1	chr11:64333972-64334416	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:64334025-64334439	PFSK-1	brain:	n/a	n/a
9	MYC	chr11:64334098-64334451	MCF10A-Er-Src	breast:	n/a	chr11:64334229-64334238
10	USF2	chr11:64334082-64334414	HepG2	liver:	n/a	n/a
11	GTF2F1	chr11:64333984-64334430	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr11:64334091-64334249	MCF10A-Er-Src	breast:	n/a	n/a
13	JUN	chr11:64333927-64334409	Hela-S3	cervix:	n/a	chr11:64334226-64334239
14	FOS	chr11:64334082-64334413	MCF10A-Er-Src	breast:	n/a	n/a
15	NFYA	chr11:64334075-64334333	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr11:64333956-64334461	ECC-1	luminal epithelium:	n/a	chr11:64334229-64334240
17	TBP	chr11:64334082-64334354	HepG2	liver:	n/a	n/a
18	JUN	chr11:64334014-64334415	HepG2	liver:	n/a	chr11:64334226-64334239
19	CEBPD	chr11:64334047-64334348	HepG2	liver:	n/a	chr11:64334229-64334240
20	MYC	chr11:64333985-64334388	K562	blood:	n/a	chr11:64334229-64334238
21	CEBPB	chr11:64334091-64334342	HepG2	liver:	n/a	chr11:64334229-64334240
22	TCF7L2	chr11:64333431-64334629	HepG2	liver:	n/a	n/a
23	CEBPB	chr11:64334028-64334470	A549	lung:	n/a	chr11:64334229-64334240
24	MAFF	chr11:64334111-64334307	HepG2	liver:	n/a	n/a
25	FOXA1	chr11:64333893-64334342	HepG2	liver:	n/a	n/a
26	MYC	chr11:64333997-64334365	MCF10A-Er-Src	breast:	n/a	chr11:64334229-64334238
27	USF1	chr11:64334008-64334431	A549	lung:	n/a	chr11:64334237-64334248
28	UBTF	chr11:64334097-64334219	K562	blood:	n/a	n/a
29	CCNT2	chr11:64333994-64334283	K562	blood:	n/a	n/a
30	CREB1	chr11:64334042-64334327	ECC-1	luminal epithelium:	n/a	n/a
31	HCFC1	chr11:64334058-64334243	K562	blood:	n/a	n/a
32	MYC	chr11:64333857-64334317	H1-hESC	embryonic stem cell:	n/a	chr11:64334229-64334238
33	USF1	chr11:64333998-64334354	K562	blood:	n/a	chr11:64334237-64334248
34	MAX	chr11:64334077-64334345	K562	blood:	n/a	chr11:64334229-64334238
35	SP1	chr11:64333934-64334414	HepG2	liver:	n/a	n/a
36	ZNF263	chr11:64334065-64334467	HEK293-T-REx	kidney:	n/a	chr11:64334263-64334272
37	NFIC	chr11:64333800-64334345	HepG2	liver:	n/a	n/a
38	USF1	chr11:64334036-64334396	SK-N-SH_RA	brain:	n/a	chr11:64334237-64334248
39	POLR2A	chr11:64333402-64334212	H1-hESC	embryonic stem cell:	n/a	n/a
40	CHD2	chr11:64334085-64334250	K562	blood:	n/a	n/a
41	USF1	chr11:64333982-64334506	ECC-1	luminal epithelium:	n/a	chr11:64334237-64334248
42	CEBPB	chr11:64334041-64334425	IMR90	lung:	n/a	chr11:64334229-64334240
43	TCF7L2	chr11:64333612-64334639	Hela-S3	cervix:	n/a	n/a
44	CUX1	chr11:64334068-64334223	K562	blood:	n/a	n/a
45	FOXA1	chr11:64333773-64334325	HepG2	liver:	n/a	n/a
46	ESR1	chr11:64333498-64334176	ECC-1	luminal epithelium:	n/a	n/a
47	CEBPB	chr11:64333971-64334515	A549	lung:	n/a	chr11:64334229-64334240
48	SMC3	chr11:64334004-64334459	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr11:64333741-64334515	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD2	chr11:64334012-64334402	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64332541..64334832-chr11:64338629..64340699,2	MCF-7	breast:
2	chr11:64321862..64324415-chr11:64333143..64334878,2	K562	blood:

Variant related genes	Relation type
SLC22A11	TF binding region
ENSG00000168065	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11231814	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11231816	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs11231822	0.97[EUR][1000 genomes]
rs12363578	0.85[ASN][1000 genomes]
rs12808503	0.87[EUR][1000 genomes]
rs17300741	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17300895	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17372915	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164495	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2277312	0.86[EUR][1000 genomes]
rs34484509	0.92[ASN][1000 genomes]
rs34812986	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759053	0.89[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3782099	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930194	0.85[ASN][1000 genomes]
rs4930420	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4930423	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4930426	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57827982	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7102027	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7124676	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71456318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7929308	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7936185	0.92[ASN][1000 genomes]
rs7940321	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7943154	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035485	chr11:64228847-64354869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Urate levels	23263486	GWAS catalog
Urate levels	20884846	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2078267	PYGM	cis	parietal	SCAN
rs2078267	EHBP1L1	cis	parietal	SCAN
rs2078267	RTN3	cis	parietal	SCAN
rs2078267	RAB3IL1	cis	parietal	SCAN
rs2078267	MARK2	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64331400-64336000	Enhancers	Placenta	Placenta
2	chr11:64332600-64335800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:64332800-64335800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:64333000-64334400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:64333000-64334600	Weak transcription	Spleen	Spleen
6	chr11:64333000-64335600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr11:64333200-64334400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:64333200-64334600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:64333200-64334800	Enhancers	K562	blood
10	chr11:64333200-64335800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr11:64333400-64334600	Enhancers	Fetal Intestine Small	intestine
12	chr11:64333400-64334800	Enhancers	Fetal Intestine Large	intestine
13	chr11:64333400-64334800	Enhancers	Fetal Thymus	thymus
14	chr11:64333400-64335200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:64333400-64336400	Enhancers	Fetal Muscle Leg	muscle
16	chr11:64333600-64334400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:64333600-64334400	Enhancers	HUVEC	blood vessel
18	chr11:64333800-64334200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr11:64333800-64334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:64333800-64334200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:64333800-64334200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:64333800-64334200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:64333800-64334400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:64333800-64334400	Weak transcription	Pancreas	Pancrea
25	chr11:64333800-64334600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr11:64333800-64334600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr11:64333800-64334600	Flanking Active TSS	A549	lung
28	chr11:64333800-64334600	Flanking Active TSS	Hela-S3	cervix
29	chr11:64333800-64334600	Flanking Active TSS	NHEK	skin
30	chr11:64334000-64334200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:64334000-64334200	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:64334000-64334200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:64334000-64334200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:64334000-64334200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr11:64334000-64334200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:64334000-64334200	Active TSS	Brain Germinal Matrix	brain
37	chr11:64334000-64334200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr11:64334000-64334200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr11:64334000-64334200	Active TSS	Stomach Smooth Muscle	stomach
40	chr11:64334000-64334200	Flanking Active TSS	HSMM	muscle
41	chr11:64334000-64334400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr11:64334000-64334400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr11:64334000-64334400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:64334000-64334400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr11:64334000-64334400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr11:64334000-64334400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:64334000-64334400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr11:64334000-64334400	Flanking Active TSS	Fetal Kidney	kidney
49	chr11:64334000-64334400	Flanking Active TSS	Fetal Lung	lung
50	chr11:64334000-64334400	Enhancers	HSMMtube	muscle

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