Variant report

Variant	rs6699159
Chromosome Location	chr1:166946072-166946073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166945300..166947626-chr1:166953556..166955132,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1041238	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10918600	1.00[GIH][hapmap]
rs10918603	1.00[GIH][hapmap]
rs10918607	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs10918608	0.84[ASN][1000 genomes]
rs11578336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11579987	0.95[GIH][hapmap]
rs11802666	0.86[ASN][1000 genomes]
rs11805946	0.86[ASN][1000 genomes]
rs12118335	0.82[ASN][1000 genomes]
rs12126991	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12131832	0.83[ASN][1000 genomes]
rs12133327	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12134016	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12564877	0.84[ASN][1000 genomes]
rs12569084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235184	0.95[GIH][hapmap]
rs2296837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2312487	0.85[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap]
rs3736988	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41269702	0.98[ASN][1000 genomes]
rs56093705	0.83[ASN][1000 genomes]
rs61447801	0.86[ASN][1000 genomes]
rs61606407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427047	0.95[GIH][hapmap]
rs6427053	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6655947	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6660048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6662130	0.86[ASN][1000 genomes]
rs6665341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669886	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6673622	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6673720	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6681562	0.83[ASN][1000 genomes]
rs6681571	0.82[ASN][1000 genomes]
rs6682062	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695162	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]
rs6695609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6696203	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6697417	0.88[ASN][1000 genomes]
rs742048	0.95[GIH][hapmap]
rs7511933	0.86[ASN][1000 genomes]
rs7518155	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]
rs7528849	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]
rs7533688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545806	1.00[GIH][hapmap]
rs7545911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6699159	RGS4	cis	parietal	SCAN
rs6699159	TBX19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166944800-166946200	Active TSS	Spleen	Spleen
2	chr1:166945400-166946400	Enhancers	HSMMtube	muscle
3	chr1:166945400-166950200	Weak transcription	HSMM	muscle
4	chr1:166945600-166946400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:166945600-166946400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:166945600-166947400	Weak transcription	GM12878-XiMat	blood
7	chr1:166945800-166946200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:166945800-166946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:166946000-166946200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:166946000-166946400	Enhancers	Right Atrium	heart
11	chr1:166946000-166947000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:166946000-166950000	Weak transcription	Left Ventricle	heart

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