Variant report

Variant	rs66676781
Chromosome Location	chr4:79473275-79473276
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	POLR2A	chr4:79472707-79473277	MCF-7	breast:	n/a	n/a
2	TBP	chr4:79472618-79473934	H1-hESC	embryonic stem cell:	n/a	chr4:79473513-79473524
3	GTF2F1	chr4:79472562-79474258	Hela-S3	cervix:	n/a	chr4:79473513-79473524
4	POLR2A	chr4:79472541-79474124	Hela-S3	cervix:	n/a	n/a
5	MAX	chr4:79472507-79473610	A549	lung:	n/a	n/a
6	TAF1	chr4:79472625-79473911	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr4:79472442-79474286	ECC-1	luminal epithelium:	n/a	chr4:79474079-79474093 chr4:79472809-79472825 chr4:79474099-79474107 chr4:79474090-79474099 chr4:79474094-79474108 chr4:79474080-79474089
8	ZNF263	chr4:79471978-79473534	HEK293-T-REx	kidney:	n/a	chr4:79472874-79472895
9	MAX	chr4:79472611-79473610	ECC-1	luminal epithelium:	n/a	n/a
10	MYC	chr4:79472796-79473317	MCF-7	breast:	n/a	n/a
11	GATA3	chr4:79473240-79474225	A549	lung:	n/a	chr4:79474091-79474101
12	BACH1	chr4:79472887-79473398	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:79472560-79474110	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr4:79472714-79473844	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr4:79472655-79473299	H1-hESC	embryonic stem cell:	n/a	n/a
16	RFX5	chr4:79472394-79474367	Hela-S3	cervix:	n/a	n/a
17	ELK1	chr4:79473209-79473939	Hela-S3	cervix:	n/a	n/a
18	JUND	chr4:79472682-79474441	H1-hESC	embryonic stem cell:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695 chr4:79473664-79473675
19	POLR2A	chr4:79472637-79473987	H1-hESC	embryonic stem cell:	n/a	n/a
20	ESR1	chr4:79472878-79473316	ECC-1	luminal epithelium:	n/a	n/a
21	SRF	chr4:79472967-79474225	MCF-7	breast:	n/a	chr4:79473727-79473740 chr4:79473725-79473742 chr4:79473726-79473741 chr4:79473727-79473738 chr4:79473723-79473741 chr4:79473725-79473743
22	CEBPB	chr4:79471771-79474597	HCT-116	colon:	n/a	n/a
23	ATF2	chr4:79473128-79474272	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr4:79472535-79475126	Hela-S3	cervix:	n/a	n/a
25	EGR1	chr4:79472962-79473369	H1-hESC	embryonic stem cell:	n/a	chr4:79473175-79473184 chr4:79473172-79473186 chr4:79473174-79473183 chr4:79473172-79473185 chr4:79473173-79473184 chr4:79473148-79473157 chr4:79473174-79473184 chr4:79473172-79473185 chr4:79473172-79473185 chr4:79473171-79473186 chr4:79473172-79473185 chr4:79473173-79473184 chr4:79473174-79473184
26	TBP	chr4:79472454-79474294	Hela-S3	cervix:	n/a	chr4:79473513-79473524
27	SRF	chr4:79472843-79474172	MCF-7	breast:	n/a	chr4:79473727-79473740 chr4:79473725-79473742 chr4:79473726-79473741 chr4:79473727-79473738 chr4:79473723-79473741 chr4:79473725-79473743
28	CHD1	chr4:79472519-79474116	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr4:79472532-79473906	ECC-1	luminal epithelium:	n/a	n/a
30	SIN3A	chr4:79472662-79474004	H1-hESC	embryonic stem cell:	n/a	chr4:79473747-79473756 chr4:79473050-79473061 chr4:79472812-79472823
31	POLR2A	chr4:79472582-79473594	MCF-7	breast:	n/a	n/a
32	SMARCC1	chr4:79472563-79474477	Hela-S3	cervix:	n/a	n/a
33	STAT1	chr4:79472593-79474564	Hela-S3	cervix:	n/a	chr4:79474029-79474037 chr4:79473666-79473675
34	POLR2A	chr4:79472556-79474159	HUVEC	blood vessel:	n/a	n/a
35	ZKSCAN1	chr4:79472701-79473990	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr4:79472330-79474551	HUVEC	blood vessel:	n/a	n/a
37	FOSL2	chr4:79473243-79473992	A549	lung:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
38	ZBTB7A	chr4:79472579-79473897	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr4:79472519-79474052	HUVEC	blood vessel:	n/a	n/a
40	RAD21	chr4:79472632-79473485	ECC-1	luminal epithelium:	n/a	chr4:79472813-79472826
41	MAX	chr4:79471803-79474045	HCT-116	colon:	n/a	n/a
42	POLR2A	chr4:79472402-79474186	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr4:79472419-79474966	MCF10A-Er-Src	breast:	n/a	n/a
44	ZBTB7A	chr4:79472584-79474063	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr4:79471841-79474919	HCT-116	colon:	n/a	n/a
46	SRF	chr4:79472618-79474165	ECC-1	luminal epithelium:	n/a	chr4:79473727-79473740 chr4:79473725-79473742 chr4:79473726-79473741 chr4:79473727-79473738 chr4:79473723-79473741 chr4:79473725-79473743
47	EGR1	chr4:79472730-79473961	HCT-116	colon:	n/a	chr4:79473175-79473184 chr4:79473172-79473186 chr4:79473174-79473183 chr4:79473172-79473185 chr4:79473173-79473184 chr4:79473148-79473157 chr4:79473174-79473184 chr4:79473172-79473185 chr4:79473172-79473185 chr4:79473171-79473186 chr4:79473172-79473185 chr4:79473173-79473184 chr4:79473174-79473184
48	SRF	chr4:79473101-79474066	ECC-1	luminal epithelium:	n/a	chr4:79473727-79473740 chr4:79473725-79473742 chr4:79473726-79473741 chr4:79473727-79473738 chr4:79473723-79473741 chr4:79473725-79473743
49	TAF1	chr4:79472515-79473844	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr4:79472348-79475914	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78977205..78980008-chr4:79470660..79474757,5	MCF-7	breast:
2	chr11:67272678..67273647-chr4:79473066..79473795,2	Hela-S3	cervix:
3	chr4:79472676..79473531-chr6:26124284..26125269,2	Hela-S3	cervix:
4	chr4:78740326..78742288-chr4:79472480..79474297,2	MCF-7	breast:
5	chr4:79471198..79473938-chr4:79857809..79860687,2	MCF-7	breast:
6	chr4:78975304..78979082-chr4:79472141..79474367,3	MCF-7	breast:

Variant related genes	Relation type
ANXA3	TF binding region
ENSG00000180573	Chromatin interaction
ENSG00000110697	Chromatin interaction
ENSG00000138767	Chromatin interaction
ENSG00000138759	Chromatin interaction
ENSG00000163291	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11098227	0.82[ASN][1000 genomes]
rs11098228	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11098229	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11936220	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11940309	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13137102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13142813	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17003337	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17003342	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34970825	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36039411	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3749482	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3749485	0.90[ASN][1000 genomes]
rs3811747	0.82[ASN][1000 genomes]
rs4563523	0.86[EUR][1000 genomes]
rs4975143	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975144	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67325389	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71611025	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9760192	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66676781	ANXA3	cis	Nerve Tibial	GTEx
rs66676781	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79472200-79474200	Active TSS	Fetal Intestine Large	intestine
2	chr4:79472200-79474400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:79472200-79474600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:79472400-79473400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
5	chr4:79472400-79473400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
6	chr4:79472400-79473400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:79472400-79473600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:79472400-79473600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:79472400-79473600	Active TSS	Colonic Mucosa	Colon
10	chr4:79472400-79473600	Active TSS	Rectal Smooth Muscle	rectum
11	chr4:79472400-79473800	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr4:79472400-79473800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr4:79472400-79474000	Active TSS	Colon Smooth Muscle	Colon
14	chr4:79472400-79474200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:79472400-79474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr4:79472400-79474200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:79472400-79474200	Active TSS	A549	lung
20	chr4:79472400-79474400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr4:79472400-79474400	Active TSS	Right Ventricle	heart
22	chr4:79472400-79474600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:79472400-79475600	Active TSS	Right Atrium	heart
24	chr4:79472600-79473400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:79472600-79473400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:79472600-79473400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:79472600-79473400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr4:79472600-79473400	Bivalent/Poised TSS	Fetal Stomach	stomach
29	chr4:79472600-79473400	Active TSS	Gastric	stomach
30	chr4:79472600-79473400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr4:79472600-79473400	Bivalent/Poised TSS	HepG2	liver
32	chr4:79472600-79473600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr4:79472600-79473600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:79472600-79473600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:79472600-79473600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr4:79472600-79473600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr4:79472600-79473600	Active TSS	Fetal Lung	lung
38	chr4:79472600-79473600	Active TSS	Lung	lung
39	chr4:79472600-79473800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr4:79472600-79473800	Active TSS	Fetal Heart	heart
41	chr4:79472600-79474200	Active TSS	Fetal Kidney	kidney
42	chr4:79472600-79474200	Active TSS	NHEK	skin
43	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:79472600-79474400	Active TSS	Psoas Muscle	Psoas
46	chr4:79472600-79474400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:79472600-79474600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:79472600-79475200	Active TSS	Left Ventricle	heart
49	chr4:79472800-79473400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:79472800-79473400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood

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