Variant report

Variant	rs3771089
Chromosome Location	chr2:188230146-188230147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10177093	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931284	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs10931285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11883913	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12464003	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12469000	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12475425	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12477273	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12479177	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619637	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621307	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12986579	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414232	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398060	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1511879	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1511884	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1528235	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17463994	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1912850	0.81[EUR][1000 genomes]
rs2349313	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2882203	0.82[CEU][hapmap]
rs3213739	0.85[CEU][hapmap]
rs3771076	0.82[CEU][hapmap]
rs3771081	0.89[CEU][hapmap]
rs3771084	0.89[CEU][hapmap];0.87[GIH][hapmap];0.80[EUR][1000 genomes]
rs3771091	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4399679	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710629	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6759535	0.92[CEU][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs7597989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7601254	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs870509	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870882	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9646807	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3771089	CALCRL	cis	cerebellum	SCAN

Chromatin state (count:20 , 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	chr2:188209800-188233400	Weak transcription	Right Ventricle	heart
4	chr2:188210800-188248000	Weak transcription	HSMMtube	muscle
5	chr2:188214600-188250800	Weak transcription	Fetal Lung	lung
6	chr2:188214600-188257800	Weak transcription	Ovary	ovary
7	chr2:188223000-188236800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:188223000-188255200	Weak transcription	Fetal Stomach	stomach
9	chr2:188223600-188244400	Weak transcription	Fetal Kidney	kidney
10	chr2:188223800-188236000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:188223800-188239600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:188223800-188242000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:188223800-188246400	Weak transcription	Left Ventricle	heart
14	chr2:188223800-188250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:188223800-188257800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:188225000-188251200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:188225800-188239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:188227600-188233800	Strong transcription	HUVEC	blood vessel
19	chr2:188228200-188238400	Weak transcription	Adipose Nuclei	Adipose
20	chr2:188228600-188237400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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