Variant report

Variant	rs4975144
Chromosome Location	chr4:79474040-79474041
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	STAT3	chr4:79473418-79474387	MCF10A-Er-Src	breast:	n/a	chr4:79474029-79474037 chr4:79473666-79473675 chr4:79474027-79474038 chr4:79474109-79474120
3	GTF2F1	chr4:79472562-79474258	Hela-S3	cervix:	n/a	chr4:79473513-79473524
4	MYC	chr4:79473508-79474141	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:79472541-79474124	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:79473994-79474120	HUVEC	blood vessel:	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	CEBPB	chr4:79474011-79474238	HepG2	liver:	n/a	n/a
9	CEBPB	chr4:79474013-79474168	K562	blood:	n/a	n/a
10	GATA3	chr4:79473240-79474225	A549	lung:	n/a	chr4:79474091-79474101
11	MAX	chr4:79472560-79474110	ECC-1	luminal epithelium:	n/a	n/a
12	RFX5	chr4:79472394-79474367	Hela-S3	cervix:	n/a	n/a
13	EP300	chr4:79473760-79474286	K562	blood:	n/a	chr4:79474079-79474093 chr4:79474099-79474107 chr4:79474090-79474099 chr4:79474094-79474108 chr4:79474080-79474089
14	CEBPB	chr4:79473538-79474223	H1-hESC	embryonic stem cell:	n/a	n/a
15	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
16	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
17	CEBPB	chr4:79471771-79474597	HCT-116	colon:	n/a	n/a
18	ATF1	chr4:79473925-79474360	K562	blood:	n/a	n/a
19	ATF2	chr4:79473128-79474272	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUN	chr4:79473545-79474247	HepG2	liver:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79474094-79474107 chr4:79473685-79473695 chr4:79473685-79473695
21	POLR2A	chr4:79472535-79475126	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr4:79473461-79474083	MCF-7	breast:	n/a	n/a
23	GATA2	chr4:79473341-79474359	HUVEC	blood vessel:	n/a	chr4:79474091-79474101
24	CEBPB	chr4:79473576-79474243	A549	lung:	n/a	n/a
25	TBP	chr4:79472454-79474294	Hela-S3	cervix:	n/a	chr4:79473513-79473524
26	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
27	CHD1	chr4:79472519-79474116	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOS	chr4:79473449-79474271	MCF10A-Er-Src	breast:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
29	GATA3	chr4:79473351-79474101	SK-N-SH	brain:	n/a	chr4:79474091-79474101
30	SMARCC1	chr4:79472563-79474477	Hela-S3	cervix:	n/a	n/a
31	STAT1	chr4:79472593-79474564	Hela-S3	cervix:	n/a	chr4:79474029-79474037 chr4:79473666-79473675
32	POLR2A	chr4:79472556-79474159	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr4:79472330-79474551	HUVEC	blood vessel:	n/a	n/a
34	GATA3	chr4:79473388-79474057	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr4:79472519-79474052	HUVEC	blood vessel:	n/a	n/a
36	JUND	chr4:79473525-79474255	HepG2	liver:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695 chr4:79473664-79473675
37	FOS	chr4:79473386-79474125	MCF10A-Er-Src	breast:	n/a	chr4:79474092-79474101 chr4:79473686-79473694 chr4:79473685-79473695 chr4:79473685-79473695
38	MAX	chr4:79471803-79474045	HCT-116	colon:	n/a	n/a
39	POLR2A	chr4:79472402-79474186	H1-hESC	embryonic stem cell:	n/a	n/a
40	NFIC	chr4:79473418-79474090	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr4:79472419-79474966	MCF10A-Er-Src	breast:	n/a	n/a
42	ZBTB7A	chr4:79472584-79474063	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr4:79471841-79474919	HCT-116	colon:	n/a	n/a
44	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
45	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
46	EP300	chr4:79473356-79474065	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr4:79472348-79475914	MCF10A-Er-Src	breast:	n/a	n/a
48	MAFK	chr4:79473291-79474105	Hela-S3	cervix:	n/a	n/a
49	SP1	chr4:79472278-79474350	HCT-116	colon:	n/a	chr4:79472883-79472897
50	SP1	chr4:79471800-79474516	HCT-116	colon:	n/a	chr4:79472883-79472897

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	chr4:79473434..79474168-chrX:16789463..16790057,2	Hela-S3	cervix:
4	chr4:78975304..78979082-chr4:79472141..79474367,3	MCF-7	breast:

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

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11098227	0.88[ASN][1000 genomes]
rs11098228	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098229	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11936220	0.84[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs11940309	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13137102	0.91[EUR][1000 genomes]
rs13142813	0.91[EUR][1000 genomes]
rs17003337	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs17003342	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34970825	0.91[EUR][1000 genomes]
rs36039411	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3749482	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3749485	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs3811747	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4563523	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975143	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66676781	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67325389	0.88[EUR][1000 genomes]
rs9760192	0.89[EUR][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
rs4975144	ANXA3	cis	lymphoblastoid	seeQTL
rs4975144	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:81 , 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	chr4:79472400-79474200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:79472400-79474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr4:79472400-79474200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:79472400-79474200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:79472400-79474200	Active TSS	A549	lung
10	chr4:79472400-79474400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr4:79472400-79474400	Active TSS	Right Ventricle	heart
12	chr4:79472400-79474600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr4:79472400-79475600	Active TSS	Right Atrium	heart
14	chr4:79472600-79474200	Active TSS	Fetal Kidney	kidney
15	chr4:79472600-79474200	Active TSS	NHEK	skin
16	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr4:79472600-79474400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:79472600-79474400	Active TSS	Psoas Muscle	Psoas
19	chr4:79472600-79474400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr4:79472600-79474600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:79472600-79475200	Active TSS	Left Ventricle	heart
22	chr4:79472800-79474200	Active TSS	Fetal Intestine Small	intestine
23	chr4:79472800-79474200	Active TSS	Stomach Mucosa	stomach
24	chr4:79472800-79474200	Active TSS	Hela-S3	cervix
25	chr4:79473200-79474800	Flanking Active TSS	HUVEC	blood vessel
26	chr4:79473400-79474200	Active TSS	Esophagus	oesophagus
27	chr4:79473400-79474200	Weak transcription	Spleen	Spleen
28	chr4:79473400-79474400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr4:79473400-79474400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
30	chr4:79473400-79474400	Weak transcription	HSMMtube	muscle
31	chr4:79473400-79475000	Weak transcription	Ovary	ovary
32	chr4:79473400-79475200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr4:79473400-79475600	Enhancers	NHLF	lung
34	chr4:79473400-79481400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:79473400-79481400	Weak transcription	HSMM	muscle
36	chr4:79473400-79481600	Weak transcription	Gastric	stomach
37	chr4:79473400-79481600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:79473400-79485400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:79473600-79474200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:79473600-79474200	Bivalent Enhancer	Fetal Thymus	thymus
41	chr4:79473600-79474200	Weak transcription	Lung	lung
42	chr4:79473600-79474200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:79473600-79474400	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr4:79473600-79474400	Enhancers	Dnd41	blood
45	chr4:79473600-79474600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:79473600-79474600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr4:79473600-79474600	Active TSS	Fetal Stomach	stomach
48	chr4:79473600-79474800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:79473600-79475000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:79473600-79478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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