Variant report

Variant	rs17366895
Chromosome Location	chr2:188238334-188238335
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11887657	0.87[EUR][1000 genomes]
rs13432953	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1398062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828975	0.81[LWK][hapmap]
rs1706287	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs17705816	0.87[EUR][1000 genomes]
rs17705846	0.87[EUR][1000 genomes]
rs2268301	1.00[CHB][hapmap]
rs28866036	0.84[EUR][1000 genomes]
rs3213738	0.90[EUR][1000 genomes]
rs3771065	1.00[CHB][hapmap]
rs3771074	1.00[CHB][hapmap]
rs3771077	0.87[EUR][1000 genomes]
rs3771083	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771088	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3771095	1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3815524	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4482438	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059768	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67285489	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6729250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67937232	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67965661	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs696574	0.89[CEU][hapmap]
rs698578	1.00[CEU][hapmap]
rs72898690	0.99[EUR][1000 genomes]
rs72900656	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900687	0.85[EUR][1000 genomes]
rs72902452	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902489	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840606	0.85[EUR][1000 genomes]
rs840617	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs858745	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs858750	0.89[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1003061	chr2:187950057-188282330	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000617	chr2:187950057-188290511	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533935	chr2:188089148-188284766	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv834487	chr2:188182556-188353363	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv875557	chr2:188219052-188370232	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv875558	chr2:188219052-188388311	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875559	chr2:188219052-188390112	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv517687	chr2:188234678-188238334	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17366895	WBSCR28	trans	cerebellum	SCAN
rs17366895	TMEM194B	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188204000-188253600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:188208800-188250400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:188210800-188248000	Weak transcription	HSMMtube	muscle
4	chr2:188214600-188250800	Weak transcription	Fetal Lung	lung
5	chr2:188214600-188257800	Weak transcription	Ovary	ovary
6	chr2:188223000-188255200	Weak transcription	Fetal Stomach	stomach
7	chr2:188223600-188244400	Weak transcription	Fetal Kidney	kidney
8	chr2:188223800-188239600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:188223800-188242000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:188223800-188246400	Weak transcription	Left Ventricle	heart
11	chr2:188223800-188250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:188223800-188257800	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:188225000-188251200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:188225800-188239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:188228200-188238400	Weak transcription	Adipose Nuclei	Adipose
16	chr2:188233800-188238600	Genic enhancers	HUVEC	blood vessel
17	chr2:188236000-188239400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:188237200-188251000	Weak transcription	Psoas Muscle	Psoas
19	chr2:188237400-188245600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:188237600-188241800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:188237600-188246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:188238000-188248000	Weak transcription	Muscle Satellite Cultured Cells	--

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