Variant report

Variant	rs9877425
Chromosome Location	chr3:159371068-159371069
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10154893	0.93[JPT][hapmap]
rs11921824	1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11921827	1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12107648	0.92[JPT][hapmap]
rs13434009	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1347671	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1347672	0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356927	0.84[JPT][hapmap]
rs1437519	0.82[JPT][hapmap]
rs1437520	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1581342	0.86[JPT][hapmap]
rs16830484	0.81[JPT][hapmap]
rs16830510	0.85[JPT][hapmap]
rs16830519	0.93[JPT][hapmap]
rs16830523	0.93[JPT][hapmap]
rs16830546	0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16830575	1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16830579	1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16830581	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830589	0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1816621	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1816622	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962890	0.92[ASN][1000 genomes]
rs1978830	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434644	0.91[ASN][1000 genomes]
rs2886621	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4494974	0.83[ASN][1000 genomes]
rs6769217	0.81[JPT][hapmap]
rs6772245	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750688	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636120	0.81[JPT][hapmap]
rs9290046	0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9290047	0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809076	1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809681	0.85[JPT][hapmap]
rs9819000	0.82[JPT][hapmap]
rs9819080	0.92[JPT][hapmap]
rs9824363	0.92[JPT][hapmap]
rs9826417	0.89[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9829310	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832970	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9833713	0.85[JPT][hapmap]
rs9842465	0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848763	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9848897	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9851700	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860690	0.86[JPT][hapmap]
rs9863199	0.86[EUR][1000 genomes]
rs9867212	1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879792	1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9881499	0.81[JPT][hapmap]
rs9881603	0.82[JPT][hapmap]
rs9882328	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9882993	0.81[JPT][hapmap]
rs9883498	0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	chr3:159356400-159379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:159370400-159372200	Weak transcription	Left Ventricle	heart
3	chr3:159370600-159371800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:159370800-159372000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:159371000-159371400	Weak transcription	Fetal Heart	heart

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