Variant report

Variant	rs1442129
Chromosome Location	chr4:90849446-90849447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1372507	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442135	0.85[CHD][hapmap]
rs1442140	0.82[CHD][hapmap]
rs2011543	0.83[EUR][1000 genomes]
rs6532205	0.85[CEU][hapmap]
rs763443	0.85[CHD][hapmap]
rs7691487	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9307077	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1442129	SNCA	cis	cerebellum	SCAN
rs1442129	DSPP	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90832000-90850400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90841600-90850000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:90843600-90849800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:90844600-90850200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:90845200-90850000	Weak transcription	Brain Germinal Matrix	brain
6	chr4:90845600-90850200	Weak transcription	Dnd41	blood
7	chr4:90846800-90849800	Strong transcription	Primary hematopoietic stem cells	blood
8	chr4:90848200-90849800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:90848200-90853600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:90848800-90850600	Weak transcription	Primary T cells from cord blood	blood
11	chr4:90849000-90850400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:90849400-90851600	Genic enhancers	HUVEC	blood vessel

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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