Variant report

Variant	rs10189554
Chromosome Location	chr2:36814033-36814034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr2:36813919-36814937	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr2:36814019-36814071	Gliobla	brain:	n/a	n/a
3	CTCF	chr2:36813988-36814075	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr2:36813981-36814095	MCF-7	breast:	n/a	n/a
5	PBX3	chr2:36813998-36814731	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr2:36813971-36814083	MCF-7	breast:	n/a	n/a
7	CTCF	chr2:36813980-36814092	MCF-7	breast:	n/a	n/a
8	CTCF	chr2:36814024-36814085	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr2:36813959-36814089	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:36813977-36814093	MCF-7	breast:	n/a	n/a
11	CTCF	chr2:36814023-36814066	A549	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36812076..36814059-chr2:36815081..36816601,2	K562	blood:
2	chr2:36812578..36815490-chr2:36816543..36819485,2	MCF-7	breast:

No data

Variant related genes	Relation type
FEZ2	TF binding region
ENSG00000256845	Chromatin interaction
ENSG00000171055	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10175266	0.89[EUR][1000 genomes]
rs10178965	0.91[EUR][1000 genomes]
rs10180760	0.89[EUR][1000 genomes]
rs10180792	0.80[EUR][1000 genomes]
rs10194100	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10197570	0.85[EUR][1000 genomes]
rs10210291	0.84[EUR][1000 genomes]
rs10469897	0.92[EUR][1000 genomes]
rs10469898	0.92[EUR][1000 genomes]
rs11124519	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11686443	0.92[EUR][1000 genomes]
rs11691600	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11691767	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11693359	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12105545	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029475	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13385408	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13398345	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13406169	0.92[EUR][1000 genomes]
rs13406184	0.92[EUR][1000 genomes]
rs13410783	0.91[EUR][1000 genomes]
rs14291	0.87[EUR][1000 genomes]
rs1523786	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1533946	0.90[EUR][1000 genomes]
rs1533947	0.87[EUR][1000 genomes]
rs1533948	0.90[EUR][1000 genomes]
rs1533949	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17019087	0.90[EUR][1000 genomes]
rs17488036	0.89[EUR][1000 genomes]
rs2022211	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2072533	0.91[EUR][1000 genomes]
rs2072534	0.91[EUR][1000 genomes]
rs2072535	0.94[EUR][1000 genomes]
rs2075226	0.90[EUR][1000 genomes]
rs2110986	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2110987	0.91[EUR][1000 genomes]
rs2160403	0.92[EUR][1000 genomes]
rs2160404	0.91[EUR][1000 genomes]
rs34392255	0.94[EUR][1000 genomes]
rs34425257	0.89[EUR][1000 genomes]
rs3770788	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3770797	0.90[EUR][1000 genomes]
rs3770799	0.90[EUR][1000 genomes]
rs3770809	0.90[EUR][1000 genomes]
rs3770811	0.90[EUR][1000 genomes]
rs55700228	0.90[EUR][1000 genomes]
rs57670037	0.84[EUR][1000 genomes]
rs6728602	0.89[EUR][1000 genomes]
rs848610	0.91[EUR][1000 genomes]
rs848611	0.90[EUR][1000 genomes]
rs848612	0.90[EUR][1000 genomes]
rs848613	0.92[EUR][1000 genomes]
rs848614	0.89[EUR][1000 genomes]
rs848616	0.88[EUR][1000 genomes]
rs848619	0.88[EUR][1000 genomes]
rs848624	0.85[EUR][1000 genomes]
rs848627	0.81[EUR][1000 genomes]
rs848629	0.86[EUR][1000 genomes]
rs848630	0.86[EUR][1000 genomes]
rs848631	0.85[EUR][1000 genomes]
rs848635	0.84[EUR][1000 genomes]
rs848636	0.84[EUR][1000 genomes]
rs848638	0.89[EUR][1000 genomes]
rs848639	0.90[EUR][1000 genomes]
rs848640	0.86[EUR][1000 genomes]
rs9917316	0.90[EUR][1000 genomes]
rs9917318	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10189554	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 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	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
3	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:36800200-36817600	Strong transcription	Liver	Liver
19	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
20	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:36801800-36814600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:36802400-36815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:36803600-36818000	Strong transcription	Dnd41	blood
30	chr2:36803800-36814600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:36804600-36814200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:36804600-36814800	Strong transcription	Primary B cells from cord blood	blood
33	chr2:36806400-36818400	Strong transcription	HepG2	liver
34	chr2:36806800-36818200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:36807200-36815200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:36807200-36818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:36807600-36816400	Weak transcription	Brain Angular Gyrus	brain
38	chr2:36807600-36823600	Weak transcription	Spleen	Spleen
39	chr2:36808000-36814200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:36808600-36818200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:36808600-36823400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:36808600-36823800	Weak transcription	Fetal Kidney	kidney
43	chr2:36808800-36814200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:36808800-36816400	Weak transcription	Brain Anterior Caudate	brain
45	chr2:36808800-36822400	Weak transcription	Stomach Mucosa	stomach
46	chr2:36808800-36823400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:36808800-36823400	Weak transcription	Small Intestine	intestine
48	chr2:36808800-36823600	Weak transcription	Aorta	Aorta
49	chr2:36809000-36823400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:36810200-36816200	Weak transcription	Fetal Heart	heart

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