Variant report

Variant	rs1998643
Chromosome Location	chr10:91618992-91618993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11593486	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770938	0.81[ASN][1000 genomes]
rs1326198	0.81[ASN][1000 genomes]
rs1326199	0.81[ASN][1000 genomes]
rs1408582	0.81[ASN][1000 genomes]
rs1408583	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17128049	0.81[ASN][1000 genomes]
rs17128178	0.81[ASN][1000 genomes]
rs2181946	0.81[ASN][1000 genomes]
rs34343174	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34768430	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35429140	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35606974	0.81[ASN][1000 genomes]
rs35663461	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740040	0.81[ASN][1000 genomes]
rs3802651	0.81[ASN][1000 genomes]
rs58933281	0.81[ASN][1000 genomes]
rs61869806	0.81[ASN][1000 genomes]
rs7098084	0.81[ASN][1000 genomes]
rs7908779	0.81[ASN][1000 genomes]
rs7908953	0.81[ASN][1000 genomes]
rs7912390	0.81[ASN][1000 genomes]
rs7921663	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv895883	chr10:91610601-92195828	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1998643	LIPJ	cis	parietal	SCAN
rs1998643	LINC00865	cis	Artery Tibial	GTEx
rs1998643	KIF20B	cis	cerebellum	SCAN
rs1998643	LINC00865	cis	Esophagus Muscularis	GTEx
rs1998643	LINC00865	cis	Thyroid	GTEx
rs1998643	RP11-248C1.3	cis	Artery Tibial	GTEx
rs1998643	TTC27	trans	parietal	SCAN
rs1998643	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs1998643	LINC00865	cis	Nerve Tibial	GTEx
rs1998643	LINC00865	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91607000-91621600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:91613800-91620400	Weak transcription	Right Atrium	heart
3	chr10:91613800-91620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr10:91617600-91620400	Weak transcription	Rectal Smooth Muscle	rectum

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