Variant report

Variant	rs10004413
Chromosome Location	chr4:90769479-90769480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10001067	0.81[EUR][1000 genomes]
rs10028246	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12331318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348224	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1372517	0.87[EUR][1000 genomes]
rs1372521	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1372522	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1442134	0.81[EUR][1000 genomes]
rs1442135	0.87[EUR][1000 genomes]
rs1442140	0.87[EUR][1000 genomes]
rs1471483	0.87[EUR][1000 genomes]
rs1822217	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1899389	0.88[EUR][1000 genomes]
rs2245801	0.80[ASN][1000 genomes]
rs2301134	0.91[EUR][1000 genomes]
rs2301135	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2583990	0.97[ASN][1000 genomes]
rs28403500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415623	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28507349	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28734152	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28777703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35424815	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756059	0.91[EUR][1000 genomes]
rs3756063	0.90[EUR][1000 genomes]
rs3806789	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58864428	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532192	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532193	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812192	0.81[EUR][1000 genomes]
rs6816736	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6817001	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6828271	0.80[EUR][1000 genomes]
rs6831847	0.89[EUR][1000 genomes]
rs6839608	0.88[EUR][1000 genomes]
rs6843084	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848181	0.88[EUR][1000 genomes]
rs763443	0.86[EUR][1000 genomes]
rs7656954	0.89[EUR][1000 genomes]
rs7671549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7672979	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680557	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7680761	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7681154	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7681440	0.87[EUR][1000 genomes]
rs7687945	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7698219	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs894280	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920624	0.80[EUR][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
rs10004413	SNCA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90759600-90771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:90768000-90769600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr4:90768000-90770400	Enhancers	HMEC	breast
4	chr4:90768400-90769800	Enhancers	NHEK	skin
5	chr4:90768600-90769600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:90768600-90769800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:90768600-90770000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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