Variant report

Variant	rs531125
Chromosome Location	chr3:78915101-78915102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1487135	0.86[CHB][hapmap]
rs162262	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162263	0.87[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs162265	0.82[JPT][hapmap]
rs162266	0.81[EUR][1000 genomes]
rs162267	0.81[EUR][1000 genomes]
rs162423	0.85[YRI][hapmap]
rs162425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162426	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162427	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs162428	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162429	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs17311057	0.85[CHB][hapmap]
rs17311169	0.86[CHB][hapmap]
rs1825760	0.86[CHB][hapmap]
rs1865863	0.80[CHB][hapmap]
rs2018432	0.86[CHB][hapmap]
rs2082973	0.86[CHB][hapmap]
rs328045	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs329805	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs329811	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs329812	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329813	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[YRI][hapmap]
rs329815	0.81[EUR][1000 genomes]
rs329817	0.81[EUR][1000 genomes]
rs329818	0.84[EUR][1000 genomes]
rs329819	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs329822	0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs329824	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs331139	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331143	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs331145	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs331149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331158	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs331161	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331162	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs331163	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331164	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331181	0.82[EUR][1000 genomes]
rs331182	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331184	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331188	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331189	0.85[EUR][1000 genomes]
rs331190	0.88[EUR][1000 genomes]
rs331199	0.83[CEU][hapmap]
rs333483	0.86[CHB][hapmap]
rs333493	0.86[CHB][hapmap]
rs333507	0.86[CHB][hapmap]
rs432141	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453354	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4681013	0.90[CEU][hapmap]
rs479956	0.87[CEU][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs498805	0.87[CEU][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs512135	0.80[ASN][1000 genomes]
rs6548600	0.83[CHB][hapmap]
rs6548601	0.81[CHB][hapmap]
rs6770452	0.86[CHB][hapmap]
rs6772919	0.81[CHB][hapmap]
rs6800782	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs7610996	0.86[CHB][hapmap];0.85[YRI][hapmap]
rs7617433	0.85[CHB][hapmap]
rs7617538	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs7629522	0.86[CHB][hapmap]
rs7650002	0.85[CHB][hapmap]
rs9866912	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78905800-78916200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:78907400-78916800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:78907600-78920200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78907800-78916200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:78912600-78916400	Weak transcription	HepG2	liver
6	chr3:78912800-78916000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:78912800-78917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:78913000-78916000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:78913200-78916400	Weak transcription	NHDF-Ad	bronchial
10	chr3:78913200-78916800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:78913200-78918600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links