Variant report

Variant	rs556820
Chromosome Location	chr3:101031535-101031536
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	chr3:101029972..101032937-chr3:101034309..101037228,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11929578	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12485950	0.83[LWK][hapmap]
rs1464361	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2176887	0.82[EUR][1000 genomes]
rs2433032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2449824	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2460721	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553414	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553420	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553421	0.81[EUR][1000 genomes]
rs2553422	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553423	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553428	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2682389	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs348877	0.91[LWK][hapmap]
rs3846092	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs472751	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs485037	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs485793	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs503252	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs503669	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs504482	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs513283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524261	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs534119	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs535779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs551395	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs554030	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];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs566292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61379928	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs63482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779775	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6791803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6809436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs72942230	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72942264	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7618600	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7638284	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7648141	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs770968	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9917699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101028000-101044200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:101028800-101032800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:101029400-101044400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:101029800-101044600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:101030200-101044200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:101030200-101044600	Weak transcription	Fetal Lung	lung
7	chr3:101030200-101045800	Weak transcription	HUVEC	blood vessel
8	chr3:101030200-101052800	Weak transcription	Fetal Stomach	stomach
9	chr3:101030400-101062400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:101030600-101032200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:101030800-101065400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:101031000-101044200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:101031400-101031800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:101031400-101032200	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links