Variant report

Variant	rs3796664
Chromosome Location	chr4:90730687-90730688
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10009760	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10030935	0.83[ASN][1000 genomes]
rs10155475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1023777	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11097234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097238	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502363	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649704	0.83[ASN][1000 genomes]
rs2119787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870028	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3796665	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3910104	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7356228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7356297	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs765517	0.83[ASN][1000 genomes]
rs7678651	0.83[ASN][1000 genomes]
rs7697570	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796664	SNCA	cis	Artery Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90706400-90733800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90709600-90732600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:90709800-90735400	Weak transcription	Ovary	ovary
4	chr4:90711800-90734000	Weak transcription	Dnd41	blood
5	chr4:90714600-90734000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:90714800-90740400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:90718800-90748000	Weak transcription	Brain Angular Gyrus	brain
8	chr4:90719000-90747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:90722400-90741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:90722600-90741400	Weak transcription	HMEC	breast
12	chr4:90723000-90741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:90723800-90731400	Weak transcription	HUVEC	blood vessel
14	chr4:90724800-90733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:90725400-90731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:90725600-90735400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:90727000-90743200	Weak transcription	Fetal Lung	lung
18	chr4:90729000-90731200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:90729000-90741600	Weak transcription	NHEK	skin
20	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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