Variant report

Variant	rs356200
Chromosome Location	chr4:90668614-90668615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10033209	0.83[CHB][hapmap]
rs10155475	0.80[JPT][hapmap]
rs11097234	0.80[JPT][hapmap]
rs12502363	0.80[JPT][hapmap]
rs189596	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119787	0.80[JPT][hapmap]
rs2736990	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs356165	0.82[JPT][hapmap]
rs356168	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356209	0.91[ASN][1000 genomes]
rs356211	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356215	0.94[ASN][1000 genomes]
rs356221	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356223	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356225	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756054	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3775423	0.86[CHD][hapmap]
rs3775424	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3822095	0.80[JPT][hapmap]
rs3857057	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3857059	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3910104	0.83[JPT][hapmap]
rs3933594	0.92[ASN][1000 genomes]
rs6848726	0.80[JPT][hapmap]
rs7356228	0.80[JPT][hapmap]
rs7661330	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs9999231	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs356200	SNCA	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90642800-90668800	Weak transcription	Brain Substantia Nigra	brain
2	chr4:90646800-90674000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:90648200-90673400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:90649400-90674000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:90649400-90696400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:90659600-90672600	Weak transcription	HUVEC	blood vessel
7	chr4:90659600-90674000	Weak transcription	HMEC	breast
8	chr4:90661600-90672600	Weak transcription	Hela-S3	cervix
9	chr4:90663400-90691400	Weak transcription	Dnd41	blood
10	chr4:90664200-90674000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:90664400-90674200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:90664600-90678000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:90664800-90674400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:90667600-90669200	Enhancers	Brain Anterior Caudate	brain
15	chr4:90668000-90669200	Enhancers	Ovary	ovary
16	chr4:90668000-90670000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:90668400-90669200	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:90668600-90669000	Enhancers	Fetal Kidney	kidney
19	chr4:90668600-90669400	Enhancers	Brain Hippocampus Middle	brain
20	chr4:90668600-90670800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:90668600-90674000	Weak transcription	Fetal Lung	lung

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