Variant report

Variant	rs2928239
Chromosome Location	chr5:5540234-5540235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11746392	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17479	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246106	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246112	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264076	0.83[EUR][1000 genomes]
rs2438486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438487	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438489	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2441069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441070	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2448438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448440	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2455471	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2455472	0.88[ASN][1000 genomes]
rs2578513	0.90[ASN][1000 genomes]
rs2578514	0.89[ASN][1000 genomes]
rs2578515	0.90[ASN][1000 genomes]
rs2578516	0.90[ASN][1000 genomes]
rs2578517	0.96[EUR][1000 genomes]
rs2578518	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578520	0.90[EUR][1000 genomes]
rs2578521	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578522	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2578523	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2578525	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2578526	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2578527	0.91[ASN][1000 genomes]
rs2578528	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2578529	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2578531	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2578532	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578533	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2578561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2591694	0.90[ASN][1000 genomes]
rs2591696	0.90[ASN][1000 genomes]
rs2591699	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591700	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2591701	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591702	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591703	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591704	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591705	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591706	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2591708	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619830	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619831	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619832	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619833	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619834	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619835	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619836	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2619837	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619839	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2619840	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2619842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619845	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2652702	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2652703	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2652704	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2652705	0.90[ASN][1000 genomes]
rs2652706	0.90[EUR][1000 genomes]
rs2652707	0.89[ASN][1000 genomes]
rs2652708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2652709	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2652710	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2652716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652722	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652724	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652725	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652726	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2652727	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2921570	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2921571	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928240	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937807	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2937808	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2937810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv596941	chr5:5511990-5636458	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv596942	chr5:5511990-5722063	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv596943	chr5:5533625-5672577	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5539400-5540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:5540000-5542400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:5540000-5542600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:5540200-5542600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:5540200-5542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:5540200-5542800	Weak transcription	H1 Cell Line	embryonic stem cell

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