Variant report

Variant	rs3775439
Chromosome Location	chr4:90709741-90709742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10002435	0.81[CEU][hapmap]
rs10003708	0.81[ASN][1000 genomes]
rs10014396	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10018362	0.81[EUR][1000 genomes]
rs10025915	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10033209	0.83[ASN][1000 genomes]
rs10433953	0.99[ASN][1000 genomes]
rs1045722	0.83[ASN][1000 genomes]
rs10516844	0.80[ASN][1000 genomes]
rs10516845	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097238	0.80[JPT][hapmap]
rs11931062	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11931074	0.80[ASN][1000 genomes]
rs11935469	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11944331	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11945223	0.81[ASN][1000 genomes]
rs12648141	0.83[ASN][1000 genomes]
rs17016071	0.83[ASN][1000 genomes]
rs2737029	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28393675	0.81[ASN][1000 genomes]
rs28412513	0.83[ASN][1000 genomes]
rs28613708	0.82[ASN][1000 genomes]
rs28781297	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35495602	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35541731	0.83[ASN][1000 genomes]
rs356165	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs356203	0.83[ASN][1000 genomes]
rs3756054	0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs3775422	0.81[ASN][1000 genomes]
rs3775423	0.83[ASN][1000 genomes]
rs3775424	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3775427	1.00[ASN][1000 genomes]
rs3775433	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3775434	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs3822086	0.83[ASN][1000 genomes]
rs3822089	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822090	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857051	0.81[ASN][1000 genomes]
rs3857052	0.82[ASN][1000 genomes]
rs3857053	0.83[ASN][1000 genomes]
rs3857057	0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs3857058	0.83[ASN][1000 genomes]
rs3857059	0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs3857061	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3899608	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4031753	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4088093	0.83[ASN][1000 genomes]
rs4088094	0.83[ASN][1000 genomes]
rs58054215	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60031383	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61032876	0.81[ASN][1000 genomes]
rs6818319	0.80[ASN][1000 genomes]
rs6822088	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826785	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6834765	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7356297	0.81[JPT][hapmap]
rs7436973	0.82[ASN][1000 genomes]
rs7655611	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7655792	0.81[ASN][1000 genomes]
rs7661330	0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs7675290	0.83[ASN][1000 genomes]
rs7681312	0.80[ASN][1000 genomes]
rs7681815	0.80[ASN][1000 genomes]
rs7684318	0.83[ASN][1000 genomes]
rs7690873	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7698672	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8180209	0.83[ASN][1000 genomes]
rs8180214	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3775439	MMRN1	cis	cerebellum	SCAN
rs3775439	MMRN1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90687200-90718400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:90697000-90711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:90703000-90712600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:90705600-90718400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:90706400-90733800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:90707800-90721400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:90709000-90710200	Enhancers	Fetal Heart	heart
8	chr4:90709200-90709800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:90709200-90709800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:90709200-90709800	Enhancers	Brain Anterior Caudate	brain
11	chr4:90709200-90709800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:90709200-90709800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:90709200-90709800	Flanking Active TSS	Fetal Lung	lung
14	chr4:90709200-90709800	Enhancers	Ovary	ovary
15	chr4:90709200-90709800	Enhancers	Right Atrium	heart
16	chr4:90709200-90710200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:90709200-90711400	Enhancers	HUVEC	blood vessel
18	chr4:90709400-90709800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:90709400-90709800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr4:90709400-90709800	Enhancers	Left Ventricle	heart
21	chr4:90709400-90710000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:90709400-90710000	Enhancers	Right Ventricle	heart
23	chr4:90709400-90710000	Enhancers	HMEC	breast
24	chr4:90709400-90710200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:90709400-90710200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:90709400-90710200	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:90709600-90732600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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