Variant report

Variant	rs36039411
Chromosome Location	chr4:79473797-79473798
allele	A/C
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	TAF1	chr4:79472625-79473911	H1-hESC	embryonic stem cell:	n/a	n/a
9	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
10	TEAD4	chr4:79473470-79473923	MCF-7	breast:	n/a	n/a
11	TFAP2A	chr4:79473338-79473999	Hela-S3	cervix:	n/a	n/a
12	GATA3	chr4:79473240-79474225	A549	lung:	n/a	chr4:79474091-79474101
13	JUND	chr4:79473508-79473806	H1-hESC	embryonic stem cell:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695 chr4:79473664-79473675
14	MAX	chr4:79472560-79474110	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr4:79472714-79473844	HUVEC	blood vessel:	n/a	n/a
16	RFX5	chr4:79472394-79474367	Hela-S3	cervix:	n/a	n/a
17	EP300	chr4:79473760-79474286	K562	blood:	n/a	chr4:79474079-79474093 chr4:79474099-79474107 chr4:79474090-79474099 chr4:79474094-79474108 chr4:79474080-79474089
18	ELK1	chr4:79473209-79473939	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr4:79473538-79474223	H1-hESC	embryonic stem cell:	n/a	n/a
20	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
21	POLR2A	chr4:79472637-79473987	H1-hESC	embryonic stem cell:	n/a	n/a
22	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
23	POLR2A	chr4:79473534-79473850	SK-N-SH	brain:	n/a	n/a
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	TEAD4	chr4:79473543-79473957	H1-hESC	embryonic stem cell:	n/a	n/a
27	ATF2	chr4:79473128-79474272	H1-hESC	embryonic stem cell:	n/a	n/a
28	CEBPB	chr4:79473561-79473927	MCF-7	breast:	n/a	n/a
29	GATA3	chr4:79473457-79473940	T-47D	breast:	n/a	n/a
30	JUN	chr4:79473545-79474247	HepG2	liver:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79474094-79474107 chr4:79473685-79473695 chr4:79473685-79473695
31	POLR2A	chr4:79472535-79475126	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr4:79473461-79474083	MCF-7	breast:	n/a	n/a
33	FOS	chr4:79473516-79473862	Hela-S3	cervix:	n/a	chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
34	GATA2	chr4:79473341-79474359	HUVEC	blood vessel:	n/a	chr4:79474091-79474101
35	GATA3	chr4:79473449-79473936	MCF-7	breast:	n/a	n/a
36	CEBPB	chr4:79473576-79474243	A549	lung:	n/a	n/a
37	TBP	chr4:79472454-79474294	Hela-S3	cervix:	n/a	chr4:79473513-79473524
38	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
39	CHD1	chr4:79472519-79474116	H1-hESC	embryonic stem cell:	n/a	n/a
40	SP1	chr4:79473479-79473995	A549	lung:	n/a	n/a
41	TAF1	chr4:79472532-79473906	ECC-1	luminal epithelium:	n/a	n/a
42	SIN3A	chr4:79472662-79474004	H1-hESC	embryonic stem cell:	n/a	chr4:79473747-79473756 chr4:79473050-79473061 chr4:79472812-79472823
43	FOS	chr4:79473449-79474271	MCF10A-Er-Src	breast:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
44	GATA3	chr4:79473351-79474101	SK-N-SH	brain:	n/a	chr4:79474091-79474101
45	TEAD4	chr4:79473410-79474038	A549	lung:	n/a	n/a
46	SMARCC1	chr4:79472563-79474477	Hela-S3	cervix:	n/a	n/a
47	STAT1	chr4:79472593-79474564	Hela-S3	cervix:	n/a	chr4:79474029-79474037 chr4:79473666-79473675
48	POLR2A	chr4:79472556-79474159	HUVEC	blood vessel:	n/a	n/a
49	ZKSCAN1	chr4:79472701-79473990	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr4:79472330-79474551	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78977205..78980008-chr4:79470660..79474757,5	MCF-7	breast:
2	chr4:78740326..78742288-chr4:79472480..79474297,2	MCF-7	breast:
3	chr4:79471198..79473938-chr4:79857809..79860687,2	MCF-7	breast:
4	chr4:79473434..79474168-chrX:16789463..16790057,2	Hela-S3	cervix:
5	chr4:78975304..78979082-chr4:79472141..79474367,3	MCF-7	breast:

Variant related genes	Relation type
ANXA3	TF binding region
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	0.84[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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13142813	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003337	0.92[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	0.93[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	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66676781	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67325389	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71611025	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9760192	0.90[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
rs36039411	ANXA3	cis	Nerve Tibial	GTEx
rs36039411	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

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	chr4:79472400-79473800	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr4:79472400-79473800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
6	chr4:79472400-79474000	Active TSS	Colon Smooth Muscle	Colon
7	chr4:79472400-79474200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:79472400-79474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr4:79472400-79474200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:79472400-79474200	Active TSS	A549	lung
13	chr4:79472400-79474400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr4:79472400-79474400	Active TSS	Right Ventricle	heart
15	chr4:79472400-79474600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:79472400-79475600	Active TSS	Right Atrium	heart
17	chr4:79472600-79473800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:79472600-79473800	Active TSS	Fetal Heart	heart
19	chr4:79472600-79474200	Active TSS	Fetal Kidney	kidney
20	chr4:79472600-79474200	Active TSS	NHEK	skin
21	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:79472600-79474400	Active TSS	Psoas Muscle	Psoas
24	chr4:79472600-79474400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr4:79472600-79474600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:79472600-79475200	Active TSS	Left Ventricle	heart
27	chr4:79472800-79473800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:79472800-79473800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr4:79472800-79473800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr4:79472800-79473800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr4:79472800-79473800	Active TSS	Brain Anterior Caudate	brain
32	chr4:79472800-79473800	Active TSS	HMEC	breast
33	chr4:79472800-79474200	Active TSS	Fetal Intestine Small	intestine
34	chr4:79472800-79474200	Active TSS	Stomach Mucosa	stomach
35	chr4:79472800-79474200	Active TSS	Hela-S3	cervix
36	chr4:79473000-79474000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
37	chr4:79473200-79473800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
38	chr4:79473200-79473800	Active TSS	Aorta	Aorta
39	chr4:79473200-79473800	Flanking Active TSS	Placenta	Placenta
40	chr4:79473200-79474800	Flanking Active TSS	HUVEC	blood vessel
41	chr4:79473400-79473800	Active TSS	Duodenum Mucosa	Duodenum
42	chr4:79473400-79474000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:79473400-79474000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr4:79473400-79474200	Active TSS	Esophagus	oesophagus
45	chr4:79473400-79474200	Weak transcription	Spleen	Spleen
46	chr4:79473400-79474400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr4:79473400-79474400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
48	chr4:79473400-79474400	Weak transcription	HSMMtube	muscle
49	chr4:79473400-79475000	Weak transcription	Ovary	ovary
50	chr4:79473400-79475200	Active TSS	Skeletal Muscle Male	skeletal muscle

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