Variant report

Variant	rs6677644
Chromosome Location	chr1:166931355-166931356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1041238	0.84[CHD][hapmap]
rs10918599	0.93[ASN][1000 genomes]
rs10918600	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10918603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10918607	0.87[CHD][hapmap]
rs11576904	0.80[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs11578336	0.87[CHD][hapmap]
rs11579987	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11583927	0.89[TSI][hapmap]
rs11588176	0.92[ASN][1000 genomes]
rs12133327	0.84[CHD][hapmap]
rs12134016	0.83[CHD][hapmap]
rs2038020	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038022	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2072742	1.00[ASN][1000 genomes]
rs2142615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2235184	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2294220	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2312675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3736988	0.84[CHD][hapmap]
rs61815130	0.91[ASN][1000 genomes]
rs61815132	0.94[ASN][1000 genomes]
rs6427047	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6427048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427053	0.84[CHD][hapmap]
rs6669886	0.81[CHB][hapmap]
rs6673622	0.83[CHD][hapmap]
rs6673720	0.84[CHD][hapmap]
rs742048	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7520897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9633326	0.80[CEU][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6677644	TBX19	cis	cerebellum	SCAN
rs6677644	UCK2	cis	cerebellum	SCAN
rs6677644	DUSP12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166919400-166936400	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:166921600-166935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:166922000-166933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:166926400-166932400	Weak transcription	Dnd41	blood
5	chr1:166926800-166934000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:166927200-166934000	Weak transcription	GM12878-XiMat	blood
7	chr1:166927200-166937200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:166927400-166941600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:166927600-166940200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:166927800-166940000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:166928600-166932400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:166931000-166931800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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