Variant report

Variant	rs10016483
Chromosome Location	chr4:78063687-78063688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10009384	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs10016676	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10018359	0.85[CEU][hapmap]
rs10026129	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs10026646	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10030735	0.84[CEU][hapmap]
rs10030867	0.84[CEU][hapmap]
rs10030957	0.85[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs10856957	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs11097704	0.88[JPT][hapmap]
rs11097730	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs11724432	0.85[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs12500115	0.96[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12504752	0.86[JPT][hapmap]
rs1477314	0.81[CEU][hapmap]
rs1559119	0.81[CEU][hapmap]
rs17397604	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2042228	0.80[CEU][hapmap]
rs28503908	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28540841	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28648488	0.81[AMR][1000 genomes]
rs4150106	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4241604	0.86[JPT][hapmap]
rs4302483	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4518274	0.86[JPT][hapmap]
rs4544732	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4576030	0.85[CEU][hapmap]
rs4859473	0.86[JPT][hapmap]
rs4859474	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859475	0.82[CEU][hapmap]
rs4859477	0.81[CEU][hapmap]
rs4859751	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859752	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs4859753	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs4859754	0.84[CEU][hapmap]
rs4859755	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs55663411	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6822794	0.81[CEU][hapmap]
rs6840915	0.85[CEU][hapmap]
rs6845599	0.85[CEU][hapmap]
rs6849124	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6849534	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6857792	0.85[CEU][hapmap]
rs729240	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438755	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7672053	0.89[ASN][1000 genomes]
rs7688769	0.89[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	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10016483	CCNG2	cis	cerebellum	SCAN
rs10016483	CXCL13	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78059000-78067200	Weak transcription	Small Intestine	intestine
2	chr4:78059200-78067200	Weak transcription	Fetal Lung	lung
3	chr4:78062400-78064400	Enhancers	Fetal Intestine Small	intestine
4	chr4:78062400-78065200	Enhancers	Fetal Intestine Large	intestine
5	chr4:78063200-78064000	Enhancers	HSMMtube	muscle
6	chr4:78063400-78063800	Enhancers	Brain Hippocampus Middle	brain
7	chr4:78063400-78064000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr4:78063600-78063800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr4:78063600-78063800	Enhancers	Pancreas	Pancrea
10	chr4:78063600-78063800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr4:78063600-78064000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:78063600-78064000	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:78063600-78064200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr4:78063600-78064600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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