Variant report

Variant	rs13092702
Chromosome Location	chr3:146119295-146119296
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLSCR2-1	chr3:146119147-146119346	NONHSAT092556
2	lnc-PLSCR2-1	chr3:146119142-146119363	NONHSAT092557

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10804713	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10804714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935626	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935631	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935632	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs11720256	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054302	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054308	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054453	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12054455	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107218	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486656	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486737	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487546	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs12487572	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492503	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12494007	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12494206	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497907	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629356	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629420	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633694	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12634107	0.86[EUR][1000 genomes]
rs13064298	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13068178	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13068800	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088225	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13090489	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403640	0.87[EUR][1000 genomes]
rs1403641	0.89[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403642	0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1403644	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1403645	0.89[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1523334	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1523335	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1523336	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1608389	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1608390	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1608391	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1608392	0.89[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17351881	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037565	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091064	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2222465	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2222466	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867865	0.85[EUR][1000 genomes]
rs2868436	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2868438	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34198003	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34359311	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34535967	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34696856	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34740686	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35082616	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35223042	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35336826	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35374128	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35695439	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234358	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4282029	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4333063	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4334615	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4355250	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4380387	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4389447	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4444684	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4476473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4558726	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4569626	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4572737	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4597678	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4600794	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4681119	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs4681120	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4681318	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681319	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681320	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681321	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681322	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681326	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs473517	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs506791	0.84[CHB][hapmap]
rs509382	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs533756	0.81[ASN][1000 genomes]
rs535344	0.81[ASN][1000 genomes]
rs544043	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs544979	0.81[ASN][1000 genomes]
rs574318	0.81[ASN][1000 genomes]
rs57545585	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58445343	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62272150	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440429	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440430	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440432	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440435	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6766583	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6766800	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6767156	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs6770000	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6774338	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6794893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6798352	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6801846	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801964	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806369	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806535	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs692749	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7431927	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7434147	0.85[EUR][1000 genomes]
rs7434212	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7614557	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617214	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7619521	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7620107	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628445	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633474	0.82[EUR][1000 genomes]
rs7645939	0.93[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7646988	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650361	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650546	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7653701	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs940193	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs955611	0.93[CEU][hapmap];0.89[CHB][hapmap]
rs9842818	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536759	chr3:146087689-146123589	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1011893	chr3:146090110-146125010	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv877617	chr3:146096182-146172109	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877618	chr3:146096182-146192324	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877619	chr3:146106142-146172109	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv877620	chr3:146109354-146172109	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	nsv877621	chr3:146117041-146172109	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146111800-146119400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:146119200-146119400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr3:146119200-146121200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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