Variant report

Variant	rs7109981
Chromosome Location	chr11:45944029-45944030
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	EP300	chr11:45943449-45944375	H1-hESC	embryonic stem cell:	n/a	chr11:45944326-45944342 chr11:45944234-45944250 chr11:45943936-45943952
2	TCF12	chr11:45943552-45944305	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr11:45942999-45944417	H1-hESC	embryonic stem cell:	n/a	chr11:45944188-45944197 chr11:45943904-45943918 chr11:45944137-45944151 chr11:45944108-45944118 chr11:45944137-45944146 chr11:45943786-45943798 chr11:45944109-45944118 chr11:45944107-45944119 chr11:45944136-45944148 chr11:45943786-45943798 chr11:45944189-45944198 chr11:45943905-45943914 chr11:45944109-45944118 chr11:45943841-45943855 chr11:45944187-45944199 chr11:45944108-45944117 chr11:45944107-45944119 chr11:45944137-45944147 chr11:45943903-45943915 chr11:45943903-45943915 chr11:45944137-45944146 chr11:45944138-45944147 chr11:45943904-45943913 chr11:45944187-45944199 chr11:45944104-45944118 chr11:45944136-45944148 chr11:45943787-45943796 chr11:45943844-45943858 chr11:45944108-45944118 chr11:45944328-45944341
4	EP300	chr11:45943523-45944084	HepG2	liver:	n/a	chr11:45943936-45943952
5	POLR2A	chr11:45944001-45944450	HCT-116	colon:	n/a	n/a
6	MAX	chr11:45943484-45945245	ECC-1	luminal epithelium:	n/a	chr11:45943840-45943850
7	SIN3A	chr11:45942868-45945276	H1-hESC	embryonic stem cell:	n/a	chr11:45944228-45944241 chr11:45944150-45944161 chr11:45943644-45943653 chr11:45943637-45943650
8	CHD2	chr11:45943548-45944107	H1-hESC	embryonic stem cell:	n/a	chr11:45943653-45943663
9	MAZ	chr11:45943407-45944542	HepG2	liver:	n/a	chr11:45943840-45943850
10	TEAD4	chr11:45943636-45944134	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFIC	chr11:45942901-45944220	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr11:45943598-45944053	ECC-1	luminal epithelium:	n/a	chr11:45943644-45943660
13	EGR1	chr11:45943798-45944409	MCF-7	breast:	n/a	chr11:45944324-45944334 chr11:45943944-45943957 chr11:45944183-45944196
14	YY1	chr11:45943436-45944743	HepG2	liver:	n/a	chr11:45944325-45944334 chr11:45943971-45943985 chr11:45943950-45943961
15	ETS1	chr11:45943989-45944332	K562	blood:	n/a	n/a
16	POLR2A	chr11:45943684-45944470	HCT-116	colon:	n/a	n/a
17	MYC	chr11:45943408-45944688	H1-hESC	embryonic stem cell:	n/a	chr11:45943840-45943850
18	SP4	chr11:45943554-45944375	H1-hESC	embryonic stem cell:	n/a	chr11:45944105-45944121 chr11:45944183-45944199 chr11:45944134-45944150 chr11:45943901-45943917 chr11:45944103-45944119
19	POLR2A	chr11:45943565-45944489	HepG2	liver:	n/a	n/a
20	YY1	chr11:45944003-45944608	H1-hESC	embryonic stem cell:	n/a	chr11:45944325-45944334
21	IRF1	chr11:45943858-45944373	K562	blood:	n/a	chr11:45943901-45943915 chr11:45944187-45944201 chr11:45944134-45944148 chr11:45944107-45944121
22	MAX	chr11:45942936-45944627	ECC-1	luminal epithelium:	n/a	chr11:45943840-45943850
23	EGR1	chr11:45943803-45944292	K562	blood:	n/a	chr11:45943944-45943957 chr11:45944183-45944196
24	GATA3	chr11:45942945-45944049	T-47D	breast:	n/a	n/a
25	POLR2A	chr11:45943113-45944443	ECC-1	luminal epithelium:	n/a	n/a
26	CHD2	chr11:45943781-45944105	HepG2	liver:	n/a	n/a
27	HMGN3	chr11:45943644-45945084	K562	blood:	n/a	n/a
28	EGR1	chr11:45943603-45944423	ECC-1	luminal epithelium:	n/a	chr11:45944324-45944334 chr11:45943944-45943957 chr11:45944183-45944196
29	CTBP2	chr11:45942964-45944255	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:45943902-45944587	SK-N-MC	brain:	n/a	n/a
31	ZEB1	chr11:45943601-45944033	GM12878	blood:	n/a	n/a
32	MYC	chr11:45943738-45945102	K562	blood:	n/a	chr11:45943840-45943850
33	EP300	chr11:45942781-45944534	ECC-1	luminal epithelium:	n/a	chr11:45942994-45943001 chr11:45944326-45944342 chr11:45944234-45944250 chr11:45943936-45943952
34	TCF7L2	chr11:45943454-45944846	HCT-116	colon:	n/a	n/a
35	NR2F2	chr11:45943674-45944443	MCF-7	breast:	n/a	n/a
36	POLR2A	chr11:45943635-45944452	HepG2	liver:	n/a	n/a
37	HEY1	chr11:45943607-45944431	HepG2	liver:	n/a	chr11:45944292-45944307 chr11:45944416-45944431
38	MAX	chr11:45943239-45944127	H1-hESC	embryonic stem cell:	n/a	chr11:45943840-45943850
39	POLR2A	chr11:45943463-45944459	H1-hESC	embryonic stem cell:	n/a	n/a
40	YY1	chr11:45943597-45944117	H1-hESC	embryonic stem cell:	n/a	chr11:45943971-45943985 chr11:45943950-45943961
41	TEAD4	chr11:45943590-45944135	H1-hESC	embryonic stem cell:	n/a	n/a
42	GTF2F1	chr11:45943603-45944245	H1-hESC	embryonic stem cell:	n/a	n/a
43	HDAC2	chr11:45943594-45944153	H1-hESC	embryonic stem cell:	n/a	n/a
44	TAF7	chr11:45944029-45944465	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr11:45942718-45945382	H1-hESC	embryonic stem cell:	n/a	n/a
46	HDAC2	chr11:45943516-45944414	MCF-7	breast:	n/a	n/a
47	SIN3AK20	chr11:45943973-45944567	K562	blood:	n/a	n/a
48	EGR1	chr11:45943512-45944559	HCT-116	colon:	n/a	chr11:45944324-45944334 chr11:45943944-45943957 chr11:45944183-45944196
49	MAX	chr11:45943461-45944820	MCF-7	breast:	n/a	chr11:45943840-45943850
50	SP4	chr11:45943670-45944269	H1-hESC	embryonic stem cell:	n/a	chr11:45944105-45944121 chr11:45944183-45944199 chr11:45944134-45944150 chr11:45943901-45943917 chr11:45944103-45944119

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:45943979-45944029	HCM	heart:	n/a
2	chr11:45943979-45944029	BJ	skin:	n/a
3	chr11:45943979-45944029	AoSMC	blood vessel:	n/a
4	chr11:45943979-45944029	HIPEpiC	eye:	n/a
5	chr11:45943979-45944029	Hepatocyte	liver:	n/a
6	chr11:45943979-45944029	HepG2	liver:	n/a
7	chr11:45943979-45944029	NB4	blood:	n/a
8	chr11:45943979-45944029	AG04449	skin:	fetal
9	chr11:45943979-45944029	PANC-1	pancreas:	n/a
10	chr11:45943979-45944029	AG10803	skin:	n/a
11	chr11:45943979-45944029	HRCEpiC	kidney:	n/a
12	chr11:45943979-45944029	GM12878	blood:	n/a
13	chr11:45943979-45944029	ECC-1	luminal epithelium:	n/a
14	chr11:45943979-45944029	RPTEC	kidney:	n/a
15	chr11:45943979-45944029	HNPCEpiC	eye:	n/a
16	chr11:45943979-45944029	HRE	kidney:	n/a
17	chr11:45943979-45944029	NH-A	brain:	n/a
18	chr11:45943979-45944029	HL-60	blood:	n/a
19	chr11:45943979-45944029	Caco-2	colon:	n/a
20	chr11:45943979-45944029	MCF10A-Er-Src	breast:	n/a
21	chr11:45943979-45944029	HCPEpiC	choroid plexus:	n/a
22	chr11:45943979-45944029	MCF-7	breast:	n/a
23	chr11:45943979-45944029	SK-N-MC	brain:	n/a
24	chr11:45943979-45944029	GM12892	blood:	n/a
25	chr11:45943979-45944029	CMK	blood:	n/a
26	chr11:45943979-45944029	HUVEC	blood vessel:	n/a
27	chr11:45943979-45944029	Jurkat	blood:	n/a
28	chr11:45943979-45944029	NT2-D1	testis:	n/a
29	chr11:45943979-45944029	PrEC	prostate:	n/a
30	chr11:45943979-45944029	GM06990	blood:	n/a
31	chr11:45943979-45944029	SAEC	small airway:	n/a
32	chr11:45943979-45944029	HAEpiC	amniotic membrane:	n/a
33	chr11:45943979-45944029	ovcar-3	ovarian:	n/a
34	chr11:45943979-45944029	H1-hESC	embryonic stem cell:	embryo
35	chr11:45943979-45944029	AG04450	lung:	fetal
36	chr11:45943979-45944029	SK-N-SH	brain:	n/a
37	chr11:45943979-45944029	LNCaP	prostate:	n/a
38	chr11:45943979-45944029	PFSK-1	brain:	n/a
39	chr11:45943979-45944029	HRPEpiC	eye:	n/a
40	chr11:45943979-45944029	AG09309	skin:	n/a
41	chr11:45943979-45944029	K562	blood:	n/a
42	chr11:45943979-45944029	HMEC	breast:	n/a
43	chr11:45943979-45944029	NHDF-neo	bronchial:	n/a
44	chr11:45943979-45944029	HCF	heart:	n/a
45	chr11:45943979-45944029	U87	brain:	n/a
46	chr11:45943979-45944029	HEEpiC	esophagus:	n/a
47	chr11:45943979-45944029	T-47D	breast:	n/a
48	chr11:45943979-45944029	SKMC	muscle:	n/a
49	chr11:45943979-45944029	BE2_C	brain:	n/a
50	chr11:45943979-45944029	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:45867151..45870859-chr11:45942545..45946514,4	K562	blood:
2	chr11:45942684..45944705-chr11:46141351..46143147,2	K562	blood:
3	chr11:45943430..45944211-chr5:39074478..39074986,2	HCT-116	colon:
4	chr11:45879680..45881437-chr11:45942342..45944046,2	MCF-7	breast:

Variant related genes	Relation type
GYLTL1B	TF binding region
PEX16	TF binding region
PEX16	CpG island
GYLTL1B	CpG island
ENSG00000164327	Chromatin interaction
ENSG00000135365	Chromatin interaction
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10838530	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838531	0.94[ASN][1000 genomes]
rs1132349	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11600112	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2271847	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2280331	0.86[ASN][1000 genomes]
rs3802758	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7124323	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7124434	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7925824	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs867813	0.96[ASN][1000 genomes]
rs939108	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1798496	chr11:45925495-45948304	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3327833	chr11:45942401-45945249	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45941200-45953400	Weak transcription	Dnd41	blood
2	chr11:45942800-45944200	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr11:45943200-45944200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
4	chr11:45943200-45945200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr11:45943200-45945400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr11:45943200-45945800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr11:45943400-45944200	Enhancers	Primary hematopoietic stem cells	blood
8	chr11:45943400-45944400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr11:45943400-45944400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr11:45943400-45944800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr11:45943400-45945000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr11:45943400-45945000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:45943400-45945000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr11:45943400-45945000	Enhancers	Fetal Heart	heart
15	chr11:45943400-45945200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr11:45943400-45945200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr11:45943400-45945200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr11:45943400-45945200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
19	chr11:45943400-45945200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr11:45943400-45945200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
21	chr11:45943400-45945400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr11:45943600-45944200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:45943600-45944200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr11:45943600-45944200	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr11:45943600-45944200	Bivalent Enhancer	Left Ventricle	heart
26	chr11:45943600-45944400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:45943600-45944400	Flanking Active TSS	Liver	Liver
28	chr11:45943600-45944400	Bivalent Enhancer	Fetal Brain Male	brain
29	chr11:45943600-45944400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr11:45943600-45944600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:45943600-45944600	Active TSS	Pancreas	Pancrea
32	chr11:45943600-45944800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr11:45943600-45944800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
34	chr11:45943600-45944800	Active TSS	Esophagus	oesophagus
35	chr11:45943600-45944800	Active TSS	Lung	lung
36	chr11:45943600-45944800	Active TSS	K562	blood
37	chr11:45943600-45945000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:45943600-45945000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
39	chr11:45943600-45945000	Flanking Bivalent TSS/Enh	Thymus	Thymus
40	chr11:45943600-45945000	Active TSS	HepG2	liver
41	chr11:45943600-45945200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr11:45943600-45945200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr11:45943600-45945200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:45943600-45945200	Flanking Active TSS	Right Ventricle	heart
45	chr11:45943600-45945400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:45943600-45945600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr11:45943800-45944200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr11:45943800-45944200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:45943800-45944200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
50	chr11:45943800-45944200	Enhancers	Rectal Mucosa Donor 29	rectum

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