Variant report

Variant	rs17414617
Chromosome Location	chr1:86495606-86495607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLCA2-1	chr1:86495537-86496272	NONHSAT004263

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10518360	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10518362	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161727	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057842	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077017	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12353970	0.91[EUR][1000 genomes]
rs12354099	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354100	0.92[ASN][1000 genomes]
rs12729890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730639	0.89[EUR][1000 genomes]
rs12743320	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12744993	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12748730	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12750946	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359419	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1698742	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698743	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698744	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405880	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405900	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406138	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406173	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406644	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17413771	0.81[EUR][1000 genomes]
rs17414498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17414519	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17414568	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17414884	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34848727	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471070	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477562	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489267	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912442	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912443	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912455	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4912459	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500756	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511363	0.95[ASN][1000 genomes]
rs511732	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516799	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518538	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519361	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521253	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532684	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538256	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs547023	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551670	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766419	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040491	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56229462	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56353901	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56392000	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567565	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567617	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs569409	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570172	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574780	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580540	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582517	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584895	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586240	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586629	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599761	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612256	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615805	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616281	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617652	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631512	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632295	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632697	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634946	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635391	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635397	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635713	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636210	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647380	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648866	0.91[EUR][1000 genomes]
rs650216	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663463	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs663901	0.95[ASN][1000 genomes]
rs664099	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664412	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6658643	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682503	1.00[ASN][1000 genomes]
rs6703328	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs679256	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680179	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72716130	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958291	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958294	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72960324	0.90[EUR][1000 genomes]
rs72960354	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7411998	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv525678	chr1:86487914-86549498	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86494200-86506800	Weak transcription	Fetal Lung	lung

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