Variant report

Variant	rs9840484
Chromosome Location	chr3:159304703-159304704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158984413..158985174-chr3:159304068..159304978,3	MCF-7	breast:
2	chr3:159039956..159040769-chr3:159304062..159305002,3	MCF-7	breast:
3	chr3:158998387..158998907-chr3:159304112..159304962,2	MCF-7	breast:
4	chr3:158981261..158982254-chr3:159304162..159305156,6	MCF-7	breast:
5	chr3:158984325..158985283-chr3:159303605..159305136,6	MCF-7	breast:
6	chr3:159039627..159040946-chr3:159304062..159304967,4	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10154893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1030882	0.85[ASN][1000 genomes]
rs11921824	0.81[JPT][hapmap]
rs11921827	0.81[JPT][hapmap]
rs12106839	0.85[ASN][1000 genomes]
rs12107648	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1343824	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1347671	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1356925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1356926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1356927	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1437519	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1437520	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1550218	1.00[CEU][hapmap]
rs1581342	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16830480	0.85[ASN][1000 genomes]
rs16830484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830487	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16830507	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16830510	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16830519	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16830523	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16830534	0.84[AMR][1000 genomes]
rs16830575	0.81[JPT][hapmap]
rs16830579	0.81[JPT][hapmap]
rs1816621	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1976819	1.00[CEU][hapmap]
rs1978830	0.81[JPT][hapmap]
rs1978831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1980254	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28743043	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2886621	0.81[JPT][hapmap]
rs3930053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs59412427	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59556163	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61018732	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61036525	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61373569	0.81[ASN][1000 genomes]
rs6768439	0.80[EUR][1000 genomes]
rs6769217	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6796636	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73012253	0.84[AMR][1000 genomes]
rs7619259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7629269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7650974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7653224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9290045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9809076	0.81[JPT][hapmap]
rs9809681	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9817830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818110	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9819000	0.90[CHB][hapmap]
rs9819080	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9821936	0.84[EUR][1000 genomes]
rs9823562	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824363	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9826416	0.80[EUR][1000 genomes]
rs9829229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9829310	0.81[JPT][hapmap]
rs9831125	0.80[EUR][1000 genomes]
rs9832443	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9833614	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs9833713	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9833762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9848763	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9848897	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9851700	0.81[JPT][hapmap]
rs9852770	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9857497	0.80[EUR][1000 genomes]
rs9860690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864641	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9870872	0.84[AMR][1000 genomes]
rs9871035	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871188	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9881603	0.90[CHB][hapmap]
rs9882328	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9882993	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159303800-159304800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:159304000-159304800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:159304000-159304800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:159304200-159304800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:159304200-159304800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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