Variant report

Variant	rs11620188
Chromosome Location	chr13:29628679-29628680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC46A3-5	chr13:29625171-29631758	NONHSAT032713

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1006810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1322383	0.80[ASN][1000 genomes]
rs1322385	0.89[ASN][1000 genomes]
rs1575301	0.84[JPT][hapmap]
rs1590277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs184467	0.82[ASN][1000 genomes]
rs2077255	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2146139	0.80[ASN][1000 genomes]
rs2146140	0.80[ASN][1000 genomes]
rs2181182	0.83[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs2181183	0.80[ASN][1000 genomes]
rs2475514	0.80[ASN][1000 genomes]
rs2475515	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2475518	0.81[JPT][hapmap]
rs2475519	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2475523	0.80[ASN][1000 genomes]
rs2475524	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2475525	0.80[ASN][1000 genomes]
rs2475537	0.83[JPT][hapmap]
rs2475550	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2475551	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2479778	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2479779	0.84[JPT][hapmap]
rs2479785	0.80[ASN][1000 genomes]
rs2479786	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2479787	0.81[JPT][hapmap]
rs2987344	0.81[JPT][hapmap]
rs326517	0.81[JPT][hapmap]
rs326524	0.91[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs326526	0.81[JPT][hapmap]
rs3751402	0.86[JPT][hapmap]
rs6490346	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs68008399	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7317087	0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7326464	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7328602	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7331544	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7332330	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7334030	0.89[ASN][1000 genomes]
rs7336281	0.86[JPT][hapmap]
rs7337190	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7339409	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs745423	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs754395	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7986144	0.89[ASN][1000 genomes]
rs7989159	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7994068	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913494	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9314927	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9314932	0.86[JPT][hapmap]
rs9506080	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9506087	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9506089	0.80[ASN][1000 genomes]
rs9508235	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9508236	0.90[ASN][1000 genomes]
rs9508238	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9508239	0.88[ASN][1000 genomes]
rs9550435	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550436	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9550437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9551598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9551599	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9551602	0.86[JPT][hapmap]
rs9578072	0.83[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3406145	chr13:29616606-29917459	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29612400-29633600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:29628200-29633600	Weak transcription	Fetal Heart	heart

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