Variant report

Variant	rs687069
Chromosome Location	chr3:59871013-59871014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11924342	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11924368	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061328	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs17061335	1.00[JPT][hapmap]
rs17061352	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061366	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061380	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061381	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061388	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17299801	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs294451	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.92[AMR][1000 genomes]
rs602197	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs604398	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs620113	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6446087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs750793	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780712	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9284900	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9311738	0.85[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs9311739	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9819258	1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9844365	0.80[AMR][1000 genomes]
rs9851805	0.83[AMR][1000 genomes]
rs9853482	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864403	1.00[JPT][hapmap]
rs9868156	0.82[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9871827	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv460565	chr3:59842644-59877988	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470616	chr3:59842644-59877988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv590385	chr3:59842644-59877988	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs687069	FEZF2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59865600-59871600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:59867600-59871400	Weak transcription	Dnd41	blood
3	chr3:59868800-59882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:59869400-59873600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:59869400-59873800	Enhancers	Primary hematopoietic stem cells	blood
6	chr3:59869600-59873400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:59869800-59873200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:59870200-59871200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:59870200-59872200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:59870200-59874000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:59870400-59871600	Enhancers	Primary T cells from cord blood	blood
12	chr3:59870400-59873600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:59870400-59874000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:59870800-59872200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:59870800-59872600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:59870800-59872600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:59871000-59871400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr3:59871000-59872000	Enhancers	Thymus	Thymus
19	chr3:59871000-59872200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:59871000-59872600	Enhancers	Fetal Thymus	thymus

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