Variant report

Variant	rs333507
Chromosome Location	chr3:78840953-78840954
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	chr3:78838533..78841279-chr3:78841928..78844326,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1033185	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11923155	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355983	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1487135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162423	0.87[CHB][hapmap]
rs162425	0.91[CHB][hapmap]
rs162428	0.87[CHB][hapmap]
rs162429	0.87[CHB][hapmap]
rs17311036	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17311057	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17311169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376753	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1825760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865860	0.82[JPT][hapmap]
rs1865861	0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1865863	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1961636	0.83[ASN][1000 genomes]
rs2018432	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2082973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329805	0.87[CHB][hapmap]
rs329812	0.86[CHB][hapmap]
rs329813	0.93[CHB][hapmap]
rs329819	0.87[CHB][hapmap]
rs331134	0.84[CHB][hapmap]
rs331149	0.84[CHB][hapmap]
rs331158	0.93[CHB][hapmap];0.83[CHD][hapmap]
rs333483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs333506	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35077320	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35556205	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681011	0.86[ASN][1000 genomes]
rs4681013	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs531125	0.86[CHB][hapmap]
rs56077922	0.81[ASN][1000 genomes]
rs57046576	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58611756	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58792018	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59263997	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6548595	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6548600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66496525	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66528054	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67488304	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67703869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6770452	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805432	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72892461	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72892501	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73113488	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73117115	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73848602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7638321	0.85[ASN][1000 genomes]
rs7650002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861603	0.83[ASN][1000 genomes]
rs9866912	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][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	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	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78826600-78843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78834200-78841200	Weak transcription	Small Intestine	intestine
3	chr3:78835000-78843600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:78835200-78843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:78838800-78843600	Weak transcription	NHEK	skin
6	chr3:78839800-78841800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:78840000-78841600	Enhancers	Brain Germinal Matrix	brain
8	chr3:78840000-78842200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:78840200-78841200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:78840400-78843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:78840600-78841400	Enhancers	Brain Anterior Caudate	brain
12	chr3:78840600-78841800	Enhancers	Brain Angular Gyrus	brain
13	chr3:78840600-78842000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:78840800-78841600	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links