Variant report

Variant	rs9868090
Chromosome Location	chr3:86927593-86927594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11127961	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11127962	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12485477	0.92[ASN][1000 genomes]
rs12488464	0.92[ASN][1000 genomes]
rs12497862	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714670	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064692	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066960	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13070989	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074432	0.86[YRI][hapmap]
rs13087636	0.92[ASN][1000 genomes]
rs13087787	0.82[YRI][hapmap]
rs13088306	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093052	0.82[ASN][1000 genomes]
rs13093618	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370038	0.82[ASN][1000 genomes]
rs4859048	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859060	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419886	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419887	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419888	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551383	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6551384	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551477	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551494	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774777	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791881	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794181	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426518	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427084	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427577	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7428262	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430324	0.92[EUR][1000 genomes]
rs7433355	0.92[EUR][1000 genomes]
rs7623510	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630422	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633281	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635070	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638201	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642134	0.92[EUR][1000 genomes]
rs7643213	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643326	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644095	0.82[EUR][1000 genomes]
rs7652100	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9284805	0.85[ASN][1000 genomes]
rs9284807	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9284808	0.86[ASN][1000 genomes]
rs9284809	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310025	0.92[ASN][1000 genomes]
rs9310026	0.86[ASN][1000 genomes]
rs9310027	0.92[ASN][1000 genomes]
rs9310028	0.92[ASN][1000 genomes]
rs9310029	0.89[ASN][1000 genomes]
rs9310030	0.92[ASN][1000 genomes]
rs9310033	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310036	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310037	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310038	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9310039	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9681197	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682104	0.88[ASN][1000 genomes]
rs9682583	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9682971	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9683172	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9683187	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9683191	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9683301	0.92[ASN][1000 genomes]
rs9683310	0.92[ASN][1000 genomes]
rs9713014	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9713018	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9713182	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9713389	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9713410	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9713421	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9713432	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9713450	0.91[EUR][1000 genomes]
rs9713459	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9713574	0.92[ASN][1000 genomes]
rs9713693	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9713794	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9756085	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9756114	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9756702	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9757447	0.92[ASN][1000 genomes]
rs9757801	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9759006	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9759053	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9799281	0.85[ASN][1000 genomes]
rs9809980	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812688	0.88[ASN][1000 genomes]
rs9826119	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9828863	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830914	0.85[ASN][1000 genomes]
rs9831416	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831548	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833690	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842925	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845020	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847167	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856526	0.85[ASN][1000 genomes]
rs9858833	0.81[AFR][1000 genomes]
rs9864034	0.92[EUR][1000 genomes]
rs9868316	0.92[EUR][1000 genomes]
rs9868576	0.85[ASN][1000 genomes]
rs9869007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869786	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9881446	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882146	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882953	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877116	chr3:86518318-86964922	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv877119	chr3:86722823-86952516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv877120	chr3:86722823-86961118	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv877123	chr3:86732817-86952516	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv519148	chr3:86831077-86995124	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv877127	chr3:86832039-86952516	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv877128	chr3:86845934-86952516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
8	nsv877129	chr3:86845934-86964922	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
9	nsv877130	chr3:86875458-86952516	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv877131	chr3:86875458-86961118	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
11	nsv963525	chr3:86920310-86948539	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86919800-86938600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:86925600-86927800	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr3:86926200-86927800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:86926600-86928400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:86927000-86927800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:86927200-86928400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:86927400-86927800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:86927400-86927800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:86927400-86927800	Enhancers	HUES48 Cell Line	embryonic stem cell

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