Variant report

Variant	rs12869557
Chromosome Location	chr13:48465342-48465343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUCLA2-4	chr13:48464985-48466403	XLOC_010601

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12873785	0.94[ASN][1000 genomes]
rs1555722	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17425881	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1974039	0.94[ASN][1000 genomes]
rs2104373	0.91[ASN][1000 genomes]
rs2104374	0.90[ASN][1000 genomes]
rs2296573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4553498	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942710	0.91[ASN][1000 genomes]
rs6561411	0.95[ASN][1000 genomes]
rs7317860	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs7323277	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7334095	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334463	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs7336952	0.99[ASN][1000 genomes]
rs7337766	0.83[CHB][hapmap];0.99[ASN][1000 genomes]
rs7981260	0.91[ASN][1000 genomes]
rs7986369	0.95[ASN][1000 genomes]
rs7989231	0.81[YRI][hapmap]
rs7993360	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7993810	0.95[ASN][1000 genomes]
rs7994427	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7998886	0.92[ASN][1000 genomes]
rs9316346	1.00[JPT][hapmap]
rs9562779	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9567940	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9567943	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9567948	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9567958	0.81[YRI][hapmap]
rs9591123	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9595813	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48453800-48471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose
4	chr13:48461000-48472200	Weak transcription	Spleen	Spleen
5	chr13:48461000-48472400	Weak transcription	Lung	lung
6	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
7	chr13:48463600-48474600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:48464600-48467400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:48464800-48469800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:48465000-48465800	Enhancers	HSMMtube	muscle
11	chr13:48465000-48467400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr13:48465000-48467400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:48465000-48484000	Weak transcription	Primary T cells from cord blood	blood
14	chr13:48465200-48466200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr13:48465200-48478200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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