Variant report

Variant	rs1706287
Chromosome Location	chr2:188224057-188224058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1011989	0.94[ASN][1000 genomes]
rs13431269	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13432953	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs1398058	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17366895	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs3771083	0.89[CEU][hapmap]
rs3771095	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs3815524	0.89[CEU][hapmap]
rs56295242	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60980181	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6729250	0.89[CEU][hapmap]
rs6753578	0.86[CEU][hapmap]
rs696573	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs696574	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698580	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698581	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs840617	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858747	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858748	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858749	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858751	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858754	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1706287	TMEM194B	cis	parietal	SCAN
rs1706287	GULP1	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr2:188209000-188229600	Weak transcription	Fetal Thymus	thymus
4	chr2:188209800-188233400	Weak transcription	Right Ventricle	heart
5	chr2:188210800-188248000	Weak transcription	HSMMtube	muscle
6	chr2:188214600-188250800	Weak transcription	Fetal Lung	lung
7	chr2:188214600-188257800	Weak transcription	Ovary	ovary
8	chr2:188215000-188224600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:188215600-188225200	Weak transcription	Esophagus	oesophagus
10	chr2:188216200-188229000	Weak transcription	Fetal Intestine Large	intestine
11	chr2:188219400-188225400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:188219600-188224200	Weak transcription	Lung	lung
13	chr2:188220200-188224400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:188220200-188224600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:188222400-188225800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:188222600-188225000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:188222600-188225800	Strong transcription	Adipose Nuclei	Adipose
18	chr2:188223000-188236800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:188223000-188255200	Weak transcription	Fetal Stomach	stomach
20	chr2:188223600-188227600	Genic enhancers	HUVEC	blood vessel
21	chr2:188223600-188244400	Weak transcription	Fetal Kidney	kidney
22	chr2:188223800-188225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:188223800-188225800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:188223800-188236000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:188223800-188239600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:188223800-188242000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:188223800-188246400	Weak transcription	Left Ventricle	heart
28	chr2:188223800-188250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:188223800-188257800	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:188224000-188225400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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