Variant report

Variant	rs13142813
Chromosome Location	chr4:79473523-79473524
allele	C/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	JUN	chr4:79473506-79474367	HUVEC	blood vessel:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79474094-79474107 chr4:79473685-79473695 chr4:79473685-79473695
2	ELF1	chr4:79473446-79473965	MCF-7	breast:	n/a	n/a
3	TBP	chr4:79472618-79473934	H1-hESC	embryonic stem cell:	n/a	chr4:79473513-79473524
4	STAT3	chr4:79473418-79474387	MCF10A-Er-Src	breast:	n/a	chr4:79474029-79474037 chr4:79473666-79473675 chr4:79474027-79474038 chr4:79474109-79474120
5	GTF2F1	chr4:79472562-79474258	Hela-S3	cervix:	n/a	chr4:79473513-79473524
6	MYC	chr4:79473508-79474141	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr4:79472541-79474124	Hela-S3	cervix:	n/a	n/a
8	MAX	chr4:79472507-79473610	A549	lung:	n/a	n/a
9	TAF1	chr4:79472625-79473911	H1-hESC	embryonic stem cell:	n/a	n/a
10	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
11	ZNF263	chr4:79471978-79473534	HEK293-T-REx	kidney:	n/a	chr4:79472874-79472895
12	MAX	chr4:79472611-79473610	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr4:79473470-79473923	MCF-7	breast:	n/a	n/a
14	TFAP2A	chr4:79473338-79473999	Hela-S3	cervix:	n/a	n/a
15	GATA3	chr4:79473240-79474225	A549	lung:	n/a	chr4:79474091-79474101
16	JUND	chr4:79473508-79473806	H1-hESC	embryonic stem cell:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695 chr4:79473664-79473675
17	MAX	chr4:79472560-79474110	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr4:79472714-79473844	HUVEC	blood vessel:	n/a	n/a
19	RFX5	chr4:79472394-79474367	Hela-S3	cervix:	n/a	n/a
20	ELK1	chr4:79473209-79473939	Hela-S3	cervix:	n/a	n/a
21	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
22	POLR2A	chr4:79472637-79473987	H1-hESC	embryonic stem cell:	n/a	n/a
23	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
24	CEBPB	chr4:79471771-79474597	HCT-116	colon:	n/a	n/a
25	GTF2F1	chr4:79473493-79473944	H1-hESC	embryonic stem cell:	n/a	chr4:79473513-79473524
26	ATF2	chr4:79473128-79474272	H1-hESC	embryonic stem cell:	n/a	n/a
27	GATA3	chr4:79473457-79473940	T-47D	breast:	n/a	n/a
28	POLR2A	chr4:79472535-79475126	Hela-S3	cervix:	n/a	n/a
29	TCF12	chr4:79473461-79474083	MCF-7	breast:	n/a	n/a
30	FOS	chr4:79473516-79473862	Hela-S3	cervix:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
31	GATA2	chr4:79473341-79474359	HUVEC	blood vessel:	n/a	chr4:79474091-79474101
32	GATA3	chr4:79473449-79473936	MCF-7	breast:	n/a	n/a
33	TBP	chr4:79472454-79474294	Hela-S3	cervix:	n/a	chr4:79473513-79473524
34	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
35	CHD1	chr4:79472519-79474116	H1-hESC	embryonic stem cell:	n/a	n/a
36	SP1	chr4:79473479-79473995	A549	lung:	n/a	n/a
37	TAF1	chr4:79472532-79473906	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3A	chr4:79472662-79474004	H1-hESC	embryonic stem cell:	n/a	chr4:79473747-79473756 chr4:79473050-79473061 chr4:79472812-79472823
39	FOS	chr4:79473449-79474271	MCF10A-Er-Src	breast:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
40	GATA3	chr4:79473351-79474101	SK-N-SH	brain:	n/a	chr4:79474091-79474101
41	TEAD4	chr4:79473410-79474038	A549	lung:	n/a	n/a
42	POLR2A	chr4:79472582-79473594	MCF-7	breast:	n/a	n/a
43	SMARCC1	chr4:79472563-79474477	Hela-S3	cervix:	n/a	n/a
44	STAT1	chr4:79472593-79474564	Hela-S3	cervix:	n/a	chr4:79474029-79474037 chr4:79473666-79473675
45	POLR2A	chr4:79472556-79474159	HUVEC	blood vessel:	n/a	n/a
46	ZKSCAN1	chr4:79472701-79473990	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr4:79472330-79474551	HUVEC	blood vessel:	n/a	n/a
48	GATA3	chr4:79473388-79474057	SK-N-SH	brain:	n/a	n/a
49	FOSL2	chr4:79473243-79473992	A549	lung:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
50	FOSL2	chr4:79473493-79473850	A549	lung:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:79473488-79473538	Jurkat	blood:	n/a
2	chr4:79473488-79473538	BJ	skin:	n/a
3	chr4:79473488-79473538	BE2_C	brain:	n/a
4	chr4:79473488-79473538	GM06990	blood:	n/a
5	chr4:79473488-79473538	GM12878	blood:	n/a
6	chr4:79473488-79473538	Hela-S3	cervix:	n/a
7	chr4:79473488-79473538	SKMC	muscle:	n/a
8	chr4:79473488-79473538	ProgFib	skin:	n/a
9	chr4:79473488-79473538	AG10803	skin:	n/a
10	chr4:79473488-79473538	PANC-1	pancreas:	n/a
11	chr4:79473488-79473538	SAEC	small airway:	n/a
12	chr4:79473488-79473538	HCF	heart:	n/a
13	chr4:79473488-79473538	HIPEpiC	eye:	n/a
14	chr4:79473488-79473538	AG04450	lung:	fetal
15	chr4:79473488-79473538	GM12892	blood:	n/a
16	chr4:79473488-79473538	HCPEpiC	choroid plexus:	n/a
17	chr4:79473488-79473538	SK-N-SH_RA	brain:	n/a
18	chr4:79473488-79473538	K562	blood:	n/a
19	chr4:79473488-79473538	HEK293	kidney:	embryo
20	chr4:79473488-79473538	H1-hESC	embryonic stem cell:	embryo
21	chr4:79473488-79473538	ECC-1	luminal epithelium:	n/a
22	chr4:79473488-79473538	HEEpiC	esophagus:	n/a
23	chr4:79473488-79473538	HNPCEpiC	eye:	n/a
24	chr4:79473488-79473538	HCM	heart:	n/a
25	chr4:79473488-79473538	HL-60	blood:	n/a
26	chr4:79473488-79473538	IMR90	lung:	fetal
27	chr4:79473488-79473538	NH-A	brain:	n/a
28	chr4:79473488-79473538	AG04449	skin:	fetal
29	chr4:79473488-79473538	NHBE	bronchial:	n/a
30	chr4:79473488-79473538	HCT-116	colon:	n/a
31	chr4:79473488-79473538	ovcar-3	ovarian:	n/a
32	chr4:79473488-79473538	PFSK-1	brain:	n/a
33	chr4:79473488-79473538	T-47D	breast:	n/a
34	chr4:79473488-79473538	HAEpiC	amniotic membrane:	n/a
35	chr4:79473488-79473538	AG09309	skin:	n/a
36	chr4:79473488-79473538	HUVEC	blood vessel:	n/a
37	chr4:79473488-79473538	AoSMC	blood vessel:	n/a
38	chr4:79473488-79473538	U87	brain:	n/a
39	chr4:79473488-79473538	SK-N-SH	brain:	n/a
40	chr4:79473488-79473538	Hepatocyte	liver:	n/a
41	chr4:79473488-79473538	A549	lung:	n/a
42	chr4:79473488-79473538	NT2-D1	testis:	n/a
43	chr4:79473488-79473538	RPTEC	kidney:	n/a
44	chr4:79473488-79473538	GM19239	blood:	n/a
45	chr4:79473488-79473538	PrEC	prostate:	n/a
46	chr4:79473488-79473538	Caco-2	colon:	n/a
47	chr4:79473488-79473538	HRE	kidney:	n/a
48	chr4:79473488-79473538	HRCEpiC	kidney:	n/a
49	chr4:79473488-79473538	HRPEpiC	eye:	n/a
50	chr4:79473488-79473538	NHDF-neo	bronchial:	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	chr4:79473434..79474168-chrX:16789463..16790057,2	Hela-S3	cervix:
7	chr4:78975304..78979082-chr4:79472141..79474367,3	MCF-7	breast:

Variant related genes	Relation type
ANXA3	TF binding region
ANXA3	CpG island
ENSG00000180573	Chromatin interaction
ENSG00000110697	Chromatin interaction
ENSG00000138759	Chromatin interaction
ENSG00000138767	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	0.84[ASN][1000 genomes]
rs11098228	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098229	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11936220	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11940309	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13137102	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17003337	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17003342	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34970825	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039411	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749482	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749485	0.92[ASN][1000 genomes]
rs3811747	0.84[ASN][1000 genomes]
rs4563523	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975143	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975144	0.91[EUR][1000 genomes]
rs66676781	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67325389	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71611025	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9760192	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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
rs13142813	ANXA3	cis	Nerve Tibial	GTEx
rs13142813	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:103 , 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	chr4:79472400-79473600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:79472400-79473600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:79472400-79473600	Active TSS	Colonic Mucosa	Colon
7	chr4:79472400-79473600	Active TSS	Rectal Smooth Muscle	rectum
8	chr4:79472400-79473800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr4:79472400-79473800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr4:79472400-79474000	Active TSS	Colon Smooth Muscle	Colon
11	chr4:79472400-79474200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:79472400-79474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:79472400-79474200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:79472400-79474200	Active TSS	A549	lung
17	chr4:79472400-79474400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr4:79472400-79474400	Active TSS	Right Ventricle	heart
19	chr4:79472400-79474600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:79472400-79475600	Active TSS	Right Atrium	heart
21	chr4:79472600-79473600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:79472600-79473600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:79472600-79473600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:79472600-79473600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr4:79472600-79473600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:79472600-79473600	Active TSS	Fetal Lung	lung
27	chr4:79472600-79473600	Active TSS	Lung	lung
28	chr4:79472600-79473800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:79472600-79473800	Active TSS	Fetal Heart	heart
30	chr4:79472600-79474200	Active TSS	Fetal Kidney	kidney
31	chr4:79472600-79474200	Active TSS	NHEK	skin
32	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:79472600-79474400	Active TSS	Psoas Muscle	Psoas
35	chr4:79472600-79474400	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr4:79472600-79474600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:79472600-79475200	Active TSS	Left Ventricle	heart
38	chr4:79472800-79473600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr4:79472800-79473600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:79472800-79473600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:79472800-79473600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:79472800-79473600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:79472800-79473600	Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr4:79472800-79473600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr4:79472800-79473600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:79472800-79473600	Bivalent/Poised TSS	Fetal Brain Female	brain
47	chr4:79472800-79473600	Active TSS	Pancreas	Pancrea
48	chr4:79472800-79473800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr4:79472800-79473800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr4:79472800-79473800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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