Variant report

Variant	rs10800276
Chromosome Location	chr1:166858941-166858942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:166851966..166853993-chr1:166858092..166859598,2	K562	blood:
2	chr1:166857954..166860551-chr1:166863597..166865926,2	K562	blood:
3	chr1:166842216..166846427-chr1:166858623..166860432,3	K562	blood:
4	chr1:166852398..166855060-chr1:166856070..166859202,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152382	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10800270	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10918599	0.87[EUR][1000 genomes]
rs10918600	0.88[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs10918603	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs11579987	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]
rs11583927	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs11584352	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12562794	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1476347	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs1543313	0.95[ASN][1000 genomes]
rs2072740	0.94[ASN][1000 genomes]
rs2075946	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap]
rs2142615	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2223221	1.00[ASN][1000 genomes]
rs2235184	0.94[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2280995	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294195	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312675	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs34381372	0.98[ASN][1000 genomes]
rs3820387	0.88[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs4656516	0.98[ASN][1000 genomes]
rs4657609	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4657612	1.00[ASN][1000 genomes]
rs4657613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61815130	0.88[EUR][1000 genomes]
rs61815132	0.87[EUR][1000 genomes]
rs6427047	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs742048	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7513457	1.00[ASN][1000 genomes]
rs7545806	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs9633326	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.99[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
rs10800276	RGS4	cis	parietal	SCAN
rs10800276	B4GALT3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166855400-166860400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:166855600-166859600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:166856600-166862000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:166857200-166859000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:166857400-166859000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:166858000-166859200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:166858400-166859400	Weak transcription	Fetal Brain Female	brain
8	chr1:166858600-166861600	Weak transcription	Colon Smooth Muscle	Colon

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