Variant report

Variant	rs848613
Chromosome Location	chr2:36814848-36814849
allele	C/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	PBX3	chr2:36813919-36814937	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr2:36814094-36814951	SK-N-SH	brain:	n/a	chr2:36814297-36814314
3	GATA3	chr2:36814190-36814873	SK-N-SH	brain:	n/a	chr2:36814241-36814257 chr2:36814244-36814253
4	EP300	chr2:36814127-36814904	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:36814170-36814952	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36812578..36815490-chr2:36816543..36819485,2	MCF-7	breast:

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

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10175266	0.83[EUR][1000 genomes]
rs10178965	0.85[EUR][1000 genomes]
rs10180760	0.83[EUR][1000 genomes]
rs10189554	0.92[EUR][1000 genomes]
rs10194100	0.83[EUR][1000 genomes]
rs10469897	0.88[EUR][1000 genomes]
rs10469898	0.88[EUR][1000 genomes]
rs11124519	0.90[EUR][1000 genomes]
rs11686443	0.85[EUR][1000 genomes]
rs11691600	0.87[EUR][1000 genomes]
rs11693359	0.90[EUR][1000 genomes]
rs12105545	0.94[EUR][1000 genomes]
rs13029475	0.90[EUR][1000 genomes]
rs13385408	0.85[EUR][1000 genomes]
rs13398345	0.83[EUR][1000 genomes]
rs13406169	0.85[EUR][1000 genomes]
rs13406184	0.85[EUR][1000 genomes]
rs13410783	0.84[EUR][1000 genomes]
rs14291	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1523786	0.85[EUR][1000 genomes]
rs1533946	0.84[EUR][1000 genomes]
rs1533947	0.81[EUR][1000 genomes]
rs1533948	0.84[EUR][1000 genomes]
rs1533949	0.81[EUR][1000 genomes]
rs17019087	0.84[EUR][1000 genomes]
rs17488036	0.82[EUR][1000 genomes]
rs2022211	0.84[EUR][1000 genomes]
rs2072533	0.85[EUR][1000 genomes]
rs2072534	0.85[EUR][1000 genomes]
rs2072535	0.89[EUR][1000 genomes]
rs2075226	0.84[EUR][1000 genomes]
rs2110986	0.84[EUR][1000 genomes]
rs2110987	0.84[EUR][1000 genomes]
rs2160403	0.85[EUR][1000 genomes]
rs2160404	0.84[EUR][1000 genomes]
rs34392255	0.86[EUR][1000 genomes]
rs34425257	0.82[EUR][1000 genomes]
rs3770788	0.86[EUR][1000 genomes]
rs3770797	0.83[EUR][1000 genomes]
rs3770799	0.83[EUR][1000 genomes]
rs3770809	0.84[EUR][1000 genomes]
rs3770811	0.84[EUR][1000 genomes]
rs55700228	0.84[EUR][1000 genomes]
rs6728602	0.82[EUR][1000 genomes]
rs848610	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs848611	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848612	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848614	0.91[EUR][1000 genomes]
rs848616	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848619	0.90[EUR][1000 genomes]
rs848624	0.87[EUR][1000 genomes]
rs848627	0.83[EUR][1000 genomes]
rs848629	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs848630	0.88[EUR][1000 genomes]
rs848631	0.87[EUR][1000 genomes]
rs848635	0.86[EUR][1000 genomes]
rs848636	0.86[EUR][1000 genomes]
rs848638	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs848639	0.93[EUR][1000 genomes]
rs848640	0.88[EUR][1000 genomes]
rs9917316	0.83[EUR][1000 genomes]
rs9917318	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs848613	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 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	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:36800200-36817600	Strong transcription	Liver	Liver
17	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
18	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:36802400-36815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:36803600-36818000	Strong transcription	Dnd41	blood
27	chr2:36806400-36818400	Strong transcription	HepG2	liver
28	chr2:36806800-36818200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:36807200-36815200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr2:36807200-36818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:36807600-36816400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:36807600-36823600	Weak transcription	Spleen	Spleen
33	chr2:36808600-36818200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:36808600-36823400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:36808600-36823800	Weak transcription	Fetal Kidney	kidney
36	chr2:36808800-36816400	Weak transcription	Brain Anterior Caudate	brain
37	chr2:36808800-36822400	Weak transcription	Stomach Mucosa	stomach
38	chr2:36808800-36823400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:36808800-36823400	Weak transcription	Small Intestine	intestine
40	chr2:36808800-36823600	Weak transcription	Aorta	Aorta
41	chr2:36809000-36823400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:36810200-36816200	Weak transcription	Fetal Heart	heart
43	chr2:36810400-36818000	Strong transcription	A549	lung
44	chr2:36810400-36818400	Strong transcription	HSMM	muscle
45	chr2:36810600-36816200	Weak transcription	NHLF	lung
46	chr2:36810600-36823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:36810800-36816000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:36810800-36822200	Weak transcription	Fetal Brain Male	brain
49	chr2:36811000-36822600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:36811400-36816000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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