Variant report

Variant	rs11579987
Chromosome Location	chr1:166889364-166889365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10800276	0.88[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs10918599	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918600	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10918603	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918607	0.88[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs11576904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11578336	0.80[CHD][hapmap];0.95[GIH][hapmap]
rs11588176	0.95[ASN][1000 genomes]
rs12562794	0.80[TSI][hapmap]
rs12569084	0.95[GIH][hapmap]
rs2038020	0.93[ASN][1000 genomes]
rs2038022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2072742	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2142615	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235184	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280995	0.82[CEU][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2294220	1.00[ASN][1000 genomes]
rs2312675	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657613	0.88[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs61815130	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61815132	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427047	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427048	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6660048	0.87[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs6677644	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6695162	0.95[GIH][hapmap]
rs6695609	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs6699159	0.95[GIH][hapmap]
rs742048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518155	0.95[GIH][hapmap]
rs7520897	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7528849	0.95[GIH][hapmap]
rs7533688	0.95[GIH][hapmap]
rs7545806	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545911	0.95[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3440434	chr1:166889153-166891701	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11579987	RGS4	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166876400-166889400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:166876800-166889400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:166879200-166889600	Weak transcription	Brain Anterior Caudate	brain
4	chr1:166879400-166889600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:166880800-166909600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:166882200-166899600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:166883400-166889800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:166884600-166889400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:166884600-166889600	Weak transcription	Placenta	Placenta
10	chr1:166887000-166890200	Enhancers	Fetal Heart	heart
11	chr1:166888000-166889800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:166888200-166889800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:166888400-166889800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:166888800-166889600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:166888800-166890600	Weak transcription	Dnd41	blood
16	chr1:166889200-166889400	Enhancers	Colon Smooth Muscle	Colon
17	chr1:166889200-166889600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:166889200-166889800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr1:166889200-166890800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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