Variant report

Variant	rs55700228
Chromosome Location	chr2:36806358-36806359
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	STAT3	chr2:36805997-36806403	MCF10A-Er-Src	breast:	n/a	chr2:36806132-36806143
2	FOXA2	chr2:36805992-36806642	A549	lung:	n/a	n/a
3	FOS	chr2:36806021-36806466	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:36805985-36806466	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:36805932-36806420	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr2:36806045-36806498	MCF10A-Er-Src	breast:	n/a	chr2:36806132-36806143
7	STAT3	chr2:36805963-36806444	MCF10A-Er-Src	breast:	n/a	chr2:36806132-36806143
8	FOS	chr2:36806011-36806479	MCF10A-Er-Src	breast:	n/a	n/a
9	HDAC2	chr2:36805996-36806467	MCF-7	breast:	n/a	chr2:36806055-36806069
10	STAT3	chr2:36806052-36806486	MCF10A-Er-Src	breast:	n/a	chr2:36806132-36806143
11	CEBPB	chr2:36806040-36806448	MCF-7	breast:	n/a	chr2:36806267-36806278
12	FOSL2	chr2:36805680-36806658	A549	lung:	n/a	n/a
13	NR2F2	chr2:36806000-36806551	MCF-7	breast:	n/a	n/a
14	ARID3A	chr2:36806069-36806463	HepG2	liver:	n/a	n/a
15	FOSL2	chr2:36806032-36806506	MCF-7	breast:	n/a	n/a
16	EP300	chr2:36805847-36806587	A549	lung:	n/a	chr2:36806089-36806099
17	HDAC2	chr2:36805865-36806547	MCF-7	breast:	n/a	chr2:36806055-36806069
18	SP1	chr2:36805834-36806754	A549	lung:	n/a	n/a
19	FOSL2	chr2:36806016-36806490	A549	lung:	n/a	n/a
20	MAX	chr2:36805463-36806770	A549	lung:	n/a	n/a
21	GATA3	chr2:36805991-36806377	T-47D	breast:	n/a	n/a
22	BCL3	chr2:36805871-36806679	A549	lung:	n/a	n/a
23	FOXA1	chr2:36805861-36806450	HepG2	liver:	n/a	n/a
24	FOSL2	chr2:36805982-36806508	MCF-7	breast:	n/a	n/a
25	NR2F2	chr2:36805974-36806385	MCF-7	breast:	n/a	n/a
26	GATA3	chr2:36805772-36806729	MCF-7	breast:	n/a	chr2:36806425-36806435
27	MYC	chr2:36806085-36806389	MCF10A-Er-Src	breast:	n/a	n/a
28	SP1	chr2:36805845-36806529	A549	lung:	n/a	n/a
29	GATA3	chr2:36805725-36806705	A549	lung:	n/a	chr2:36806425-36806435
30	TCF12	chr2:36805774-36806756	A549	lung:	n/a	n/a
31	GATA3	chr2:36805844-36806573	MCF-7	breast:	n/a	chr2:36806425-36806435
32	SIN3AK20	chr2:36805787-36806633	MCF-7	breast:	n/a	n/a
33	ZNF217	chr2:36806035-36806431	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
FEZ2	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10175266	0.87[EUR][1000 genomes]
rs10178965	0.89[EUR][1000 genomes]
rs10180760	0.88[EUR][1000 genomes]
rs10189554	0.90[EUR][1000 genomes]
rs10194100	0.88[EUR][1000 genomes]
rs10197570	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10210291	0.86[EUR][1000 genomes]
rs10469897	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10469898	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124519	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11686443	0.90[EUR][1000 genomes]
rs11691600	0.96[EUR][1000 genomes]
rs11693359	0.91[EUR][1000 genomes]
rs1179494	0.93[ASN][1000 genomes]
rs12105545	0.89[EUR][1000 genomes]
rs13029475	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13385408	0.94[EUR][1000 genomes]
rs13398345	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13406169	0.90[EUR][1000 genomes]
rs13406184	0.90[EUR][1000 genomes]
rs13410783	0.88[EUR][1000 genomes]
rs14291	0.89[EUR][1000 genomes]
rs1523786	0.96[EUR][1000 genomes]
rs1533946	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1533947	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1533948	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1533949	0.86[EUR][1000 genomes]
rs17019087	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17488036	0.93[EUR][1000 genomes]
rs2022211	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072533	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072534	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072535	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075226	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110986	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110987	0.89[EUR][1000 genomes]
rs2160403	0.90[EUR][1000 genomes]
rs2160404	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34392255	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34425257	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755196	0.81[EUR][1000 genomes]
rs3770788	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770797	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770799	0.87[EUR][1000 genomes]
rs3770809	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770811	0.89[EUR][1000 genomes]
rs57670037	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728602	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848610	0.83[EUR][1000 genomes]
rs848611	0.81[EUR][1000 genomes]
rs848612	0.81[EUR][1000 genomes]
rs848613	0.84[EUR][1000 genomes]
rs848614	0.82[EUR][1000 genomes]
rs848616	0.89[EUR][1000 genomes]
rs848617	0.93[ASN][1000 genomes]
rs848619	0.91[EUR][1000 genomes]
rs848624	0.90[EUR][1000 genomes]
rs848627	0.86[EUR][1000 genomes]
rs848629	0.90[EUR][1000 genomes]
rs848630	0.91[EUR][1000 genomes]
rs848631	0.90[EUR][1000 genomes]
rs848635	0.90[EUR][1000 genomes]
rs848636	0.89[EUR][1000 genomes]
rs848638	0.88[EUR][1000 genomes]
rs848639	0.88[EUR][1000 genomes]
rs848640	0.93[EUR][1000 genomes]
rs9917316	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9917318	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55700228	FEZ2	cis	multi-tissue	Pritchard
rs55700228	FEZ2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:36789200-36807000	Weak transcription	Aorta	Aorta
4	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
5	chr2:36790400-36806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:36790800-36812000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:36791000-36807600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:36791800-36810400	Weak transcription	Right Atrium	heart
9	chr2:36792000-36806600	Weak transcription	Spleen	Spleen
10	chr2:36792200-36810400	Weak transcription	Colonic Mucosa	Colon
11	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:36792800-36811400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:36793200-36806600	Weak transcription	Esophagus	oesophagus
14	chr2:36793200-36811200	Weak transcription	Pancreas	Pancrea
15	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:36795800-36809600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:36796200-36807400	Weak transcription	Ovary	ovary
19	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:36797000-36807400	Weak transcription	Fetal Heart	heart
21	chr2:36797000-36808200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:36797600-36808800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:36798000-36809600	Strong transcription	HSMM	muscle
26	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:36798400-36806400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:36798600-36806600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:36798800-36811200	Weak transcription	Gastric	stomach
32	chr2:36799000-36806600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:36799200-36812800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:36799400-36812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:36799600-36806400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:36800200-36810400	Strong transcription	Osteobl	bone
43	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr2:36800200-36817600	Strong transcription	Liver	Liver
45	chr2:36800400-36806400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:36800400-36807000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:36800600-36807000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:36800600-36807800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:36800600-36809000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:36800800-36808600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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