Variant report

Variant	rs12049507
Chromosome Location	chr1:79790405-79790406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFI44-1	chr1:79790384-79790534	XLOC_000267
2	lnc-ELTD1-5	chr1:79790271-79790552	XLOC_000881
3	lnc-IFI44-1	chr1:79790270-79790552	NONHSAT004094
4	lnc-IFI44-1	chr1:79790385-79790548	ENSG00000235011.2
5	lnc-ELTD1-5	chr1:79790271-79790416	NONHSAT004093

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10158555	0.93[ASN][1000 genomes]
rs10489649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10874029	0.93[ASN][1000 genomes]
rs11162657	1.00[AFR][1000 genomes]
rs12023367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12024442	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12024774	0.93[ASN][1000 genomes]
rs12024949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12025007	0.87[ASN][1000 genomes]
rs12025109	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12025643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12026006	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12026857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12026964	0.85[ASN][1000 genomes]
rs12026969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12027492	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027821	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028115	0.87[ASN][1000 genomes]
rs12028685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12030013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12031186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12032517	0.93[ASN][1000 genomes]
rs12033889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12034005	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12035431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12036705	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12036905	1.00[AMR][1000 genomes]
rs12038491	1.00[AFR][1000 genomes]
rs12039243	1.00[AFR][1000 genomes]
rs12039488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12039867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12039920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12039923	1.00[AMR][1000 genomes]
rs12040033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12040121	1.00[AMR][1000 genomes]
rs12040237	1.00[AMR][1000 genomes]
rs12040880	1.00[AMR][1000 genomes]
rs12041180	1.00[AFR][1000 genomes]
rs12042159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12043955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12044503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12044515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12044901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12045663	1.00[AMR][1000 genomes]
rs12045991	1.00[AMR][1000 genomes]
rs12046684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12046976	0.87[ASN][1000 genomes]
rs12048398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12077125	0.93[ASN][1000 genomes]
rs12088382	0.93[ASN][1000 genomes]
rs1331715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1412140	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2132054	1.00[AMR][1000 genomes]
rs28370400	0.93[ASN][1000 genomes]
rs5003964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72941396	0.87[ASN][1000 genomes]
rs72943084	0.93[ASN][1000 genomes]
rs72943085	0.93[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	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv871182	chr1:79614989-79822735	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870962	chr1:79755185-79835066	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3364783	chr1:79786074-79815088	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	esv3384616	chr1:79788134-79814492	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79789800-79790600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:79789800-79790600	Weak transcription	NHDF-Ad	bronchial
3	chr1:79790000-79790800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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