Variant report

Variant	rs554030
Chromosome Location	chr3:101000966-101000967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11929578	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1464361	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2433032	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2449824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2460721	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553414	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553420	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553422	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553423	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553428	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2682387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682389	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3846092	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs472751	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs485037	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs485793	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503252	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503669	0.89[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs504482	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs513283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs524261	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs534119	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs535779	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs551395	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs556820	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs565914	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs566292	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379928	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs63482	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6779775	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6791803	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6809436	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs72942230	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72942264	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7618600	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7638284	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7648141	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs770968	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917699	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100958800-101012800	Weak transcription	Left Ventricle	heart
2	chr3:100989400-101018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:100994800-101008800	Weak transcription	Primary T cells from cord blood	blood
4	chr3:100999000-101007200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:100999200-101014600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:101000400-101001000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:101000400-101001000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:101000400-101001000	Enhancers	Fetal Stomach	stomach
9	chr3:101000600-101001200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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