Variant report

Variant	rs10469897
Chromosome Location	chr2:36818377-36818378
allele	C/T
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	POLR2A	chr2:36818351-36818435	ProgFib	skin:	n/a	n/a
2	GATA3	chr2:36818264-36818435	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:36816372..36820679-chr2:36821932..36827532,8	K562	blood:
2	chr2:36809435..36813840-chr2:36817141..36820574,5	K562	blood:
3	chr2:36817392..36820041-chr2:36820581..36825790,5	MCF-7	breast:

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

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10175266	0.87[EUR][1000 genomes]
rs10178965	0.89[EUR][1000 genomes]
rs10179862	0.80[CHB][hapmap]
rs10180760	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10180792	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10189554	0.92[EUR][1000 genomes]
rs10194100	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs10197570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10210291	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs10469898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124519	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11686443	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs11691600	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11691767	0.82[CEU][hapmap]
rs11693359	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1179494	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12105545	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs12712508	0.85[CHB][hapmap]
rs13029475	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13385408	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13398345	0.85[EUR][1000 genomes]
rs13406169	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13406184	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13410783	0.88[EUR][1000 genomes]
rs14291	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1523786	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1533946	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533947	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1533948	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533949	0.85[EUR][1000 genomes]
rs17019087	0.85[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs17488036	0.84[EUR][1000 genomes]
rs2022211	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072533	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072534	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075226	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2110986	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2110987	0.88[EUR][1000 genomes]
rs2160403	0.87[EUR][1000 genomes]
rs2160404	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34392255	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34425257	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770788	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770797	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770799	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs3770809	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770811	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5003670	0.82[EUR][1000 genomes]
rs55700228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57670037	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728602	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848603	0.90[CHB][hapmap]
rs848605	0.90[CHB][hapmap]
rs848606	0.80[CHB][hapmap]
rs848607	0.90[CHB][hapmap]
rs848610	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs848611	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs848612	0.89[EUR][1000 genomes]
rs848613	0.88[EUR][1000 genomes]
rs848614	0.83[EUR][1000 genomes]
rs848616	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs848617	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs848619	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs848624	0.81[EUR][1000 genomes]
rs848629	0.81[EUR][1000 genomes]
rs848630	0.82[EUR][1000 genomes]
rs848631	0.81[EUR][1000 genomes]
rs848635	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs848636	0.84[CEU][hapmap]
rs848638	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs848639	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs848640	0.81[EUR][1000 genomes]
rs848643	0.90[CHB][hapmap]
rs981355	0.90[CHB][hapmap]
rs9917316	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9917318	0.86[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
rs10469897	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 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	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:36806400-36818400	Strong transcription	HepG2	liver
9	chr2:36807600-36823600	Weak transcription	Spleen	Spleen
10	chr2:36808600-36823400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:36808600-36823800	Weak transcription	Fetal Kidney	kidney
12	chr2:36808800-36822400	Weak transcription	Stomach Mucosa	stomach
13	chr2:36808800-36823400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:36808800-36823400	Weak transcription	Small Intestine	intestine
15	chr2:36808800-36823600	Weak transcription	Aorta	Aorta
16	chr2:36809000-36823400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:36810400-36818400	Strong transcription	HSMM	muscle
18	chr2:36810600-36823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:36810800-36822200	Weak transcription	Fetal Brain Male	brain
20	chr2:36811000-36822600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:36811400-36821800	Weak transcription	Colonic Mucosa	Colon
22	chr2:36811400-36822600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:36811400-36822600	Weak transcription	Gastric	stomach
24	chr2:36811400-36823400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:36811400-36823600	Weak transcription	Right Ventricle	heart
26	chr2:36811600-36818400	Strong transcription	Placenta	Placenta
27	chr2:36811600-36822200	Weak transcription	Thymus	Thymus
28	chr2:36811800-36823600	Weak transcription	Pancreas	Pancrea
29	chr2:36812000-36823400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:36812200-36818400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:36812200-36821800	Weak transcription	NHEK	skin
32	chr2:36812200-36822200	Weak transcription	Esophagus	oesophagus
33	chr2:36812200-36822200	Weak transcription	Ovary	ovary
34	chr2:36812200-36822600	Weak transcription	Brain Germinal Matrix	brain
35	chr2:36812200-36823200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:36812200-36823200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:36812200-36823400	Weak transcription	Lung	lung
38	chr2:36812200-36824000	Weak transcription	HSMMtube	muscle
39	chr2:36812400-36821800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:36812400-36822000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:36813400-36823600	Weak transcription	Hela-S3	cervix
42	chr2:36814600-36821800	Weak transcription	GM12878-XiMat	blood
43	chr2:36814600-36823000	Weak transcription	Left Ventricle	heart
44	chr2:36814600-36823400	Weak transcription	Fetal Stomach	stomach
45	chr2:36815000-36822800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:36815600-36818600	Strong transcription	Primary B cells from cord blood	blood
47	chr2:36815600-36823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:36815800-36818400	Strong transcription	NH-A	brain
49	chr2:36816400-36818400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:36816400-36819200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle

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