Variant report

Variant	rs2408858
Chromosome Location	chr13:53919555-53919556
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OLFM4-9	chr13:53919346-53920093	NONHSAT034018

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1156006	0.91[ASN][1000 genomes]
rs11618497	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322949	0.81[CHB][hapmap]
rs1322951	0.81[CHB][hapmap]
rs1342669	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1373273	0.86[ASN][1000 genomes]
rs1373276	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373277	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1373281	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1418617	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1443905	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443914	0.86[AFR][1000 genomes]
rs1530399	0.82[ASN][1000 genomes]
rs1923771	0.81[CHB][hapmap]
rs2053609	0.82[ASN][1000 genomes]
rs2165985	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2197303	0.81[ASN][1000 genomes]
rs2813573	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4883678	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4884411	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7322098	0.86[ASN][1000 genomes]
rs7328151	0.94[ASN][1000 genomes]
rs7329909	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7336192	0.81[ASN][1000 genomes]
rs7985119	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7985545	0.81[ASN][1000 genomes]
rs7987501	0.88[EUR][1000 genomes]
rs7992723	0.82[CHB][hapmap]
rs7997746	0.80[EUR][1000 genomes]
rs8001044	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8002970	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316613	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536378	0.81[CHB][hapmap]
rs9536405	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536406	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568838	0.91[ASN][1000 genomes]
rs9568839	0.91[ASN][1000 genomes]

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	nsv1050969	chr13:53665927-54064861	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2756368	chr13:53824599-53923599	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53917600-53919600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:53918200-53919800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr13:53918400-53919600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr13:53918600-53919600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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