Variant report

Variant	rs6890248
Chromosome Location	chr5:42175166-42175167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42164889..42166959-chr5:42173984..42175632,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10037143	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10050512	0.89[EUR][1000 genomes]
rs10052738	1.00[CEU][hapmap]
rs10054119	0.84[EUR][1000 genomes]
rs10060873	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064990	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10073423	0.89[EUR][1000 genomes]
rs10078494	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10079521	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10461734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461736	0.89[EUR][1000 genomes]
rs10462034	0.87[EUR][1000 genomes]
rs1073273	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1110874	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1119855	0.84[ASN][1000 genomes]
rs11954853	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12153093	0.89[EUR][1000 genomes]
rs12514243	0.86[ASN][1000 genomes]
rs12515833	0.81[ASN][1000 genomes]
rs12517161	0.86[ASN][1000 genomes]
rs12519296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12522095	0.93[ASN][1000 genomes]
rs13189999	0.88[EUR][1000 genomes]
rs1354108	0.99[EUR][1000 genomes]
rs1393017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1393018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1501513	0.99[EUR][1000 genomes]
rs1501515	1.00[ASN][1000 genomes]
rs1501516	1.00[EUR][1000 genomes]
rs1501517	1.00[EUR][1000 genomes]
rs1501518	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1501519	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17586526	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17586540	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1827329	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1827330	0.99[EUR][1000 genomes]
rs1827331	1.00[EUR][1000 genomes]
rs1875430	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1909950	0.98[ASN][1000 genomes]
rs1909951	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1995351	0.98[EUR][1000 genomes]
rs2134102	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276289	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs276290	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs276291	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs34035285	0.86[EUR][1000 genomes]
rs34813199	0.84[EUR][1000 genomes]
rs35005365	0.86[EUR][1000 genomes]
rs35707555	0.87[EUR][1000 genomes]
rs36072701	0.86[ASN][1000 genomes]
rs3885984	0.89[EUR][1000 genomes]
rs3913458	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3913459	0.96[EUR][1000 genomes]
rs4242098	0.88[EUR][1000 genomes]
rs4305644	0.87[EUR][1000 genomes]
rs4320267	0.86[EUR][1000 genomes]
rs4404722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4457090	0.87[EUR][1000 genomes]
rs4460174	0.97[EUR][1000 genomes]
rs4489104	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4533937	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4626371	0.81[ASN][1000 genomes]
rs4957203	0.98[EUR][1000 genomes]
rs4957204	0.98[EUR][1000 genomes]
rs4957449	1.00[CHB][hapmap]
rs4957464	0.81[ASN][1000 genomes]
rs58911119	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6451592	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6451605	0.81[EUR][1000 genomes]
rs6861819	0.87[EUR][1000 genomes]
rs6872878	0.88[EUR][1000 genomes]
rs6888449	0.89[EUR][1000 genomes]
rs7379247	0.86[ASN][1000 genomes]
rs7713544	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7715104	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7715374	0.86[EUR][1000 genomes]
rs7718368	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs905097	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs905099	0.81[ASN][1000 genomes]
rs9292843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292848	0.84[EUR][1000 genomes]
rs931230	0.81[ASN][1000 genomes]
rs990898	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv4813	chr5:42157598-42202029	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6890248	OR10V1	trans	cerebellum	SCAN
rs6890248	ABCA4	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42173800-42175200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:42173800-42175400	Active TSS	Adipose Nuclei	Adipose

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