Variant report

Variant	rs1726746
Chromosome Location	chr11:73882260-73882261
allele	G/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	POLR2A	chr11:73881541-73882737	GM12892	blood:	n/a	n/a
2	CREB1	chr11:73881779-73882555	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr11:73881753-73882693	H1-hESC	embryonic stem cell:	n/a	n/a
4	SPI1	chr11:73882088-73882363	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:73880935-73882779	H1-neurons	neurons:	n/a	n/a
6	ELF1	chr11:73881673-73882672	MCF-7	breast:	n/a	chr11:73881977-73881988
7	POLR2A	chr11:73881747-73882660	GM12878	blood:	n/a	n/a
8	E2F4	chr11:73881752-73882434	MCF10A-Er-Src	breast:	n/a	chr11:73881894-73881906 chr11:73882108-73882117 chr11:73882010-73882027 chr11:73881917-73881926
9	SIX5	chr11:73881795-73882364	K562	blood:	n/a	chr11:73882041-73882055 chr11:73882043-73882052 chr11:73882045-73882054
10	NFIC	chr11:73882001-73882699	GM12878	blood:	n/a	n/a
11	NFIC	chr11:73881789-73882771	ECC-1	luminal epithelium:	n/a	n/a
12	REST	chr11:73882119-73882642	HL-60	blood:	n/a	chr11:73882348-73882357
13	POLR2A	chr11:73881695-73882690	SK-N-SH	brain:	n/a	n/a
14	ELF1	chr11:73881706-73882526	SK-N-SH	brain:	n/a	chr11:73881977-73881988
15	TAF1	chr11:73882122-73882734	K562	blood:	n/a	n/a
16	IRF3	chr11:73882137-73882550	HepG2	liver:	n/a	n/a
17	RAD21	chr11:73881629-73882541	Hela-S3	cervix:	n/a	n/a
18	PAX5	chr11:73882119-73882539	GM12892	blood:	n/a	chr11:73882270-73882279
19	CTCF	chr11:73881978-73882353	IMR90	lung:	n/a	chr11:73882096-73882109 chr11:73882173-73882186
20	CTCF	chr11:73882160-73882310	BE2_C	brain:	n/a	chr11:73882173-73882186
21	CEBPB	chr11:73881925-73882583	K562	blood:	n/a	n/a
22	YY1	chr11:73881701-73882637	SK-N-SH_RA	brain:	n/a	n/a
23	IRF4	chr11:73882005-73882622	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr11:73881764-73882486	PFSK-1	brain:	n/a	n/a
25	ZC3H11A	chr11:73881977-73882770	K562	blood:	n/a	n/a
26	CEBPB	chr11:73881968-73882388	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr11:73881586-73882681	GM12891	blood:	n/a	n/a
28	YY1	chr11:73881702-73882677	ECC-1	luminal epithelium:	n/a	n/a
29	CTCF	chr11:73882120-73882270	GM12874	blood:	n/a	chr11:73882173-73882186
30	SP4	chr11:73881949-73882706	H1-hESC	embryonic stem cell:	n/a	chr11:73882172-73882183
31	POLR2A	chr11:73881763-73882586	K562	blood:	n/a	n/a
32	GTF2F1	chr11:73881982-73882799	H1-hESC	embryonic stem cell:	n/a	n/a
33	TCF12	chr11:73882005-73882534	GM12878	blood:	n/a	n/a
34	GABPA	chr11:73881889-73882619	H1-hESC	embryonic stem cell:	n/a	chr11:73882104-73882118 chr11:73882107-73882121 chr11:73882107-73882116 chr11:73882107-73882118
35	BCLAF1	chr11:73881780-73882589	GM12878	blood:	n/a	chr11:73881941-73881954 chr11:73882270-73882279 chr11:73881938-73881951
36	USF2	chr11:73882249-73882520	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:73882139-73882658	HepG2	liver:	n/a	n/a
38	RAD21	chr11:73881676-73882748	A549	lung:	n/a	n/a
39	REST	chr11:73882113-73882749	MCF-7	breast:	n/a	chr11:73882348-73882357
40	FOXA1	chr11:73881846-73882585	HepG2	liver:	n/a	n/a
41	PML	chr11:73881826-73882737	K562	blood:	n/a	chr11:73882010-73882018
42	NFIC	chr11:73881788-73882586	HepG2	liver:	n/a	n/a
43	CTCF	chr11:73882120-73882270	BJ	skin:	n/a	chr11:73882173-73882186
44	MAX	chr11:73881589-73882668	NB4	blood:	n/a	n/a
45	POLR2A	chr11:73882072-73882643	HepG2	liver:	n/a	n/a
46	GTF2B	chr11:73882049-73882646	K562	blood:	n/a	n/a
47	MAX	chr11:73882149-73882659	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIX5	chr11:73881541-73882862	A549	lung:	n/a	chr11:73882041-73882055 chr11:73882043-73882052 chr11:73882045-73882054
49	SIX5	chr11:73881894-73882312	H1-hESC	embryonic stem cell:	n/a	chr11:73882041-73882055 chr11:73882043-73882052 chr11:73882045-73882054
50	CTCF	chr11:73882062-73882513	MCF-7	breast:	n/a	chr11:73882096-73882109 chr11:73882173-73882186

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:73882219-73882269	HRCEpiC	kidney:	n/a
2	chr11:73882219-73882269	A549	lung:	n/a
3	chr11:73882219-73882269	ProgFib	skin:	n/a
4	chr11:73882219-73882269	U87	brain:	n/a
5	chr11:73882219-73882269	NH-A	brain:	n/a
6	chr11:73882219-73882269	GM12891	blood:	n/a
7	chr11:73882219-73882269	ovcar-3	ovarian:	n/a
8	chr11:73882219-73882269	BJ	skin:	n/a
9	chr11:73882219-73882269	GM06990	blood:	n/a
10	chr11:73882219-73882269	HEK293	kidney:	embryo
11	chr11:73882219-73882269	GM12892	blood:	n/a
12	chr11:73882219-73882269	HEEpiC	esophagus:	n/a
13	chr11:73882219-73882269	CMK	blood:	n/a
14	chr11:73882219-73882269	Hepatocyte	liver:	n/a
15	chr11:73882219-73882269	AG09319	gingival:	n/a
16	chr11:73882219-73882269	HRE	kidney:	n/a
17	chr11:73882219-73882269	SKMC	muscle:	n/a
18	chr11:73882219-73882269	NHBE	bronchial:	n/a
19	chr11:73882219-73882269	K562	blood:	n/a
20	chr11:73882219-73882269	SK-N-SH_RA	brain:	n/a
21	chr11:73882219-73882269	HNPCEpiC	eye:	n/a
22	chr11:73882219-73882269	AG04450	lung:	fetal
23	chr11:73882219-73882269	HL-60	blood:	n/a
24	chr11:73882219-73882269	HCF	heart:	n/a
25	chr11:73882219-73882269	NB4	blood:	n/a
26	chr11:73882219-73882269	HRPEpiC	eye:	n/a
27	chr11:73882219-73882269	PANC-1	pancreas:	n/a
28	chr11:73882219-73882269	GM12878	blood:	n/a
29	chr11:73882219-73882269	IMR90	lung:	fetal
30	chr11:73882219-73882269	MCF10A-Er-Src	breast:	n/a
31	chr11:73882219-73882269	AG04449	skin:	fetal
32	chr11:73882219-73882269	RPTEC	kidney:	n/a
33	chr11:73882219-73882269	AoSMC	blood vessel:	n/a
34	chr11:73882219-73882269	HMEC	breast:	n/a
35	chr11:73882219-73882269	H1-hESC	embryonic stem cell:	embryo
36	chr11:73882219-73882269	HPAEpiC	pulmonary alveolar:	n/a
37	chr11:73882219-73882269	SK-N-MC	brain:	n/a
38	chr11:73882219-73882269	PFSK-1	brain:	n/a
39	chr11:73882219-73882269	HIPEpiC	eye:	n/a
40	chr11:73882219-73882269	Caco-2	colon:	n/a
41	chr11:73882219-73882269	GM19239	blood:	n/a
42	chr11:73882219-73882269	AG09309	skin:	n/a
43	chr11:73882219-73882269	ECC-1	luminal epithelium:	n/a
44	chr11:73882219-73882269	HCM	heart:	n/a
45	chr11:73882219-73882269	HCPEpiC	choroid plexus:	n/a
46	chr11:73882219-73882269	HUVEC	blood vessel:	n/a
47	chr11:73882219-73882269	Jurkat	blood:	n/a
48	chr11:73882219-73882269	SAEC	small airway:	n/a
49	chr11:73882219-73882269	LNCaP	prostate:	n/a
50	chr11:73882219-73882269	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73800042..73802110-chr11:73880491..73883383,2	MCF-7	breast:
2	chr11:73882131..73882865-chrX:48754645..48755172,2	Hela-S3	cervix:
3	chr11:73694022..73695981-chr11:73881444..73883965,2	MCF-7	breast:
4	chr11:73675574..73678297-chr11:73881586..73883661,2	K562	blood:
5	chr11:73692800..73696318-chr11:73880815..73883748,5	MCF-7	breast:
6	chr11:73693723..73696564-chr11:73880690..73883464,7	K562	blood:
7	chr11:73691455..73695821-chr11:73881160..73884452,10	K562	blood:
8	chr11:73780255..73782526-chr11:73881717..73883400,2	MCF-7	breast:

Variant related genes	Relation type
PPME1	TF binding region
C2CD3	TF binding region
C2CD3	CpG island
PPME1	CpG island
ENSG00000175567	Chromatin interaction
ENSG00000126768	Chromatin interaction
ENSG00000255847	Chromatin interaction
ENSG00000187726	Chromatin interaction
ENSG00000168014	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898954	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1614299	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1615115	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1685355	0.91[JPT][hapmap]
rs1726735	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1726744	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1726745	0.91[JPT][hapmap]
rs1726751	0.89[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1726752	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1726764	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs1783537	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1790381	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790398	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790399	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790404	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075577	0.91[JPT][hapmap]
rs2848559	1.00[YRI][hapmap]
rs3018184	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs474280	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[YRI][hapmap]
rs474835	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs486577	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[YRI][hapmap]
rs490539	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[YRI][hapmap]
rs4944036	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4944038	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944878	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500608	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs556134	1.00[YRI][hapmap]
rs575096	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs588097	0.91[JPT][hapmap]
rs590336	0.91[JPT][hapmap]
rs627354	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs635441	0.91[JPT][hapmap]
rs647126	0.91[JPT][hapmap]
rs6592545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6592551	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7121868	0.82[EUR][1000 genomes]
rs7483884	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7926165	0.91[JPT][hapmap]
rs826033	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs826039	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs826056	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826061	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826062	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs826066	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1726746	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73880200-73886600	Active TSS	HSMMtube	muscle
2	chr11:73880400-73883000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:73880600-73883600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr11:73880600-73883600	Active TSS	Right Atrium	heart
5	chr11:73880600-73883600	Active TSS	A549	lung
6	chr11:73880600-73883800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:73880800-73883000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:73880800-73883200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:73880800-73883400	Active TSS	Esophagus	oesophagus
10	chr11:73880800-73883400	Active TSS	Left Ventricle	heart
11	chr11:73880800-73883600	Active TSS	Aorta	Aorta
12	chr11:73880800-73883600	Active TSS	Fetal Muscle Trunk	muscle
13	chr11:73880800-73884200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr11:73881000-73883200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr11:73881000-73883200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:73881000-73883200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:73881000-73883200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr11:73881000-73883400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:73881000-73883400	Active TSS	Fetal Intestine Large	intestine
20	chr11:73881200-73882800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr11:73881200-73882800	Active TSS	Brain Germinal Matrix	brain
22	chr11:73881200-73882800	Active TSS	Rectal Smooth Muscle	rectum
23	chr11:73881200-73883000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr11:73881200-73883000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr11:73881200-73883000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:73881200-73883000	Active TSS	Fetal Heart	heart
27	chr11:73881200-73883000	Active TSS	Fetal Intestine Small	intestine
28	chr11:73881200-73883000	Active TSS	Fetal Muscle Leg	muscle
29	chr11:73881200-73883000	Active TSS	Gastric	stomach
30	chr11:73881200-73883000	Active TSS	Lung	lung
31	chr11:73881200-73883000	Active TSS	Ovary	ovary
32	chr11:73881200-73883200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr11:73881200-73883200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr11:73881200-73883200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:73881200-73883200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:73881200-73883200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:73881200-73883200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:73881200-73883200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:73881200-73883200	Active TSS	Colonic Mucosa	Colon
40	chr11:73881200-73883200	Bivalent/Poised TSS	HepG2	liver
41	chr11:73881200-73883200	Active TSS	NHDF-Ad	bronchial
42	chr11:73881200-73883400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:73881200-73883400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:73881200-73883400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:73881200-73883400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:73881200-73883400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:73881200-73883400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr11:73881200-73883400	Active TSS	Psoas Muscle	Psoas
49	chr11:73881200-73883400	Active TSS	Right Ventricle	heart
50	chr11:73881200-73883400	Active TSS	NHEK	skin

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