Variant report

Variant	rs1372510
Chromosome Location	chr4:90817259-90817260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10001067	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11097239	0.98[ASN][1000 genomes]
rs11941110	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941682	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372508	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1442134	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1442136	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904350	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119785	0.86[ASN][1000 genomes]
rs2289515	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775475	0.84[ASN][1000 genomes]
rs3775479	0.84[ASN][1000 genomes]
rs4522832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812192	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6812593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814221	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6814481	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6824979	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356205	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693616	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1372510	SNCA	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90815400-90818200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:90815600-90817400	Flanking Active TSS	Dnd41	blood
3	chr4:90815600-90817800	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr4:90815600-90817800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr4:90815800-90817400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:90815800-90820600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:90816400-90817400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:90816400-90818800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:90816400-90822200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:90816600-90817400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:90816600-90819200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:90816600-90819400	Active TSS	HUVEC	blood vessel
13	chr4:90816600-90819600	Weak transcription	Spleen	Spleen
14	chr4:90816800-90817400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr4:90816800-90817400	Active TSS	Thymus	Thymus
16	chr4:90816800-90817400	Enhancers	GM12878-XiMat	blood
17	chr4:90816800-90818800	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr4:90816800-90819400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:90816800-90819600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:90817000-90817400	Active TSS	Primary B cells from cord blood	blood
21	chr4:90817000-90817400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr4:90817000-90817400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr4:90817200-90817400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:90817200-90819600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:90817200-90819600	Weak transcription	Fetal Thymus	thymus

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