Variant report

Variant	rs990898
Chromosome Location	chr5:42153168-42153169
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OXCT1-1	chr5:42153043-42153776	XLOC_004800
2	lnc-OXCT1-1	chr5:42153043-42153776	XLOC_004800
3	lnc-OXCT1-1	chr5:42153043-42153776	XLOC_004800
4	lnc-FBXO4-1	chr5:42153042-42153776	NONHSAT101190

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10037143	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10050512	0.87[EUR][1000 genomes]
rs10052738	1.00[CEU][hapmap]
rs10054119	0.82[EUR][1000 genomes]
rs10060873	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10064990	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10073423	0.87[EUR][1000 genomes]
rs10078494	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079521	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461734	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10461735	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10461736	0.87[EUR][1000 genomes]
rs10462034	0.85[EUR][1000 genomes]
rs1073273	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110874	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1119855	0.98[ASN][1000 genomes]
rs11954853	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12153093	0.87[EUR][1000 genomes]
rs12514243	1.00[ASN][1000 genomes]
rs12515833	0.95[ASN][1000 genomes]
rs12517161	1.00[ASN][1000 genomes]
rs12519296	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13189999	0.86[EUR][1000 genomes]
rs1354108	0.97[EUR][1000 genomes]
rs1393017	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1393018	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1501513	0.99[EUR][1000 genomes]
rs1501515	0.86[ASN][1000 genomes]
rs1501516	0.98[EUR][1000 genomes]
rs1501517	0.98[EUR][1000 genomes]
rs1501518	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1501519	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1501528	0.91[ASN][1000 genomes]
rs17586491	0.80[ASN][1000 genomes]
rs17586526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17586540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1827329	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1827330	0.97[EUR][1000 genomes]
rs1827331	0.98[EUR][1000 genomes]
rs1875430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1909950	0.85[ASN][1000 genomes]
rs1909951	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1995351	1.00[EUR][1000 genomes]
rs202299	0.82[ASN][1000 genomes]
rs2134102	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161581	0.82[ASN][1000 genomes]
rs276233	0.86[ASN][1000 genomes]
rs276234	0.86[ASN][1000 genomes]
rs276237	0.86[ASN][1000 genomes]
rs276238	0.81[ASN][1000 genomes]
rs276239	0.86[ASN][1000 genomes]
rs276240	0.86[ASN][1000 genomes]
rs276242	0.86[ASN][1000 genomes]
rs276243	0.86[ASN][1000 genomes]
rs276246	0.86[ASN][1000 genomes]
rs276270	0.87[ASN][1000 genomes]
rs276277	0.89[ASN][1000 genomes]
rs276289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs276290	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs276291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs276294	0.82[ASN][1000 genomes]
rs276306	0.82[ASN][1000 genomes]
rs276307	0.82[ASN][1000 genomes]
rs276309	0.80[ASN][1000 genomes]
rs276311	0.82[ASN][1000 genomes]
rs276315	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs34035285	0.84[EUR][1000 genomes]
rs35005365	0.84[EUR][1000 genomes]
rs35707555	0.85[EUR][1000 genomes]
rs3885984	0.87[EUR][1000 genomes]
rs3913458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913459	0.98[EUR][1000 genomes]
rs4242098	0.86[EUR][1000 genomes]
rs4305644	0.85[EUR][1000 genomes]
rs4320267	0.84[EUR][1000 genomes]
rs4342369	0.82[ASN][1000 genomes]
rs4358567	0.82[ASN][1000 genomes]
rs4401612	0.89[ASN][1000 genomes]
rs4404722	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457090	0.85[EUR][1000 genomes]
rs4460174	0.94[EUR][1000 genomes]
rs4489104	0.94[EUR][1000 genomes]
rs4533937	0.94[EUR][1000 genomes]
rs4590218	0.82[ASN][1000 genomes]
rs4626371	0.95[ASN][1000 genomes]
rs4957190	0.82[ASN][1000 genomes]
rs4957191	0.82[ASN][1000 genomes]
rs4957192	0.82[ASN][1000 genomes]
rs4957203	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4957204	1.00[EUR][1000 genomes]
rs4957446	0.82[ASN][1000 genomes]
rs4957447	0.82[ASN][1000 genomes]
rs4957449	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4957464	0.95[ASN][1000 genomes]
rs58911119	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451589	0.82[ASN][1000 genomes]
rs6451592	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666080	0.86[ASN][1000 genomes]
rs6861819	0.85[EUR][1000 genomes]
rs6872878	0.86[EUR][1000 genomes]
rs6888449	0.87[EUR][1000 genomes]
rs6890248	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7341123	0.82[ASN][1000 genomes]
rs7708373	0.82[ASN][1000 genomes]
rs7708493	0.82[ASN][1000 genomes]
rs7713544	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715104	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7715374	0.84[EUR][1000 genomes]
rs7718368	0.94[EUR][1000 genomes]
rs905097	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905099	0.95[ASN][1000 genomes]
rs9292843	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9292848	0.82[EUR][1000 genomes]
rs931230	0.95[ASN][1000 genomes]
rs931231	0.82[ASN][1000 genomes]

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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised 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	113 gene(s)	inside rSNPs	diseases
3	nsv1032171	chr5:42015138-42220940	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv462125	chr5:42019110-42192620	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv597885	chr5:42019110-42192620	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1034208	chr5:42119128-42290759	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv969219	chr5:42147728-42169988	ZNF genes & repeats Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42152600-42158400	Weak transcription	Adipose Nuclei	Adipose
2	chr5:42152800-42156600	Weak transcription	Fetal Heart	heart
3	chr5:42153000-42153400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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