Variant report

Variant	rs12649400
Chromosome Location	chr4:87409142-87409143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11097111	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11938088	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs11939109	0.86[JPT][hapmap]
rs12500955	0.94[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs12503051	0.83[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12508801	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12512698	0.86[JPT][hapmap]
rs12644920	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs17011731	0.85[JPT][hapmap]
rs17011843	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs17011890	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs17011950	0.94[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs2199307	0.86[JPT][hapmap]
rs2869444	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2904095	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4235079	0.85[JPT][hapmap]
rs4235080	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4488910	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6531925	0.86[JPT][hapmap]
rs6856688	0.86[JPT][hapmap]
rs7669675	0.85[JPT][hapmap]

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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12649400	SNCA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87404600-87414800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:87405000-87418400	Weak transcription	Fetal Kidney	kidney
3	chr4:87405800-87411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87405800-87412400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:87405800-87413600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:87405800-87414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:87406800-87414200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:87407000-87417000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:87407600-87422600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:87408400-87411800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:87408400-87414200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:87409000-87409400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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