Variant report

Variant	rs2562490
Chromosome Location	chr19:21653950-21653951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1027585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1027586	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1027587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414463	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420451	0.85[AFR][1000 genomes]
rs10426240	0.82[AFR][1000 genomes]
rs1500399	0.82[AFR][1000 genomes]
rs1963611	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1983017	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1983018	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1983019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2009347	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2013529	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs2088760	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2090708	1.00[AMR][1000 genomes]
rs2090709	1.00[AMR][1000 genomes]
rs2173725	0.82[AFR][1000 genomes]
rs2255010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2255100	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562418	0.81[AFR][1000 genomes]
rs2562431	0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2562437	0.82[AFR][1000 genomes]
rs2562463	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562475	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562476	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562477	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562478	0.90[AFR][1000 genomes]
rs2562479	0.89[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562480	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562481	0.87[AFR][1000 genomes]
rs2562482	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562486	0.89[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562488	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562494	1.00[AMR][1000 genomes]
rs2562503	1.00[AMR][1000 genomes]
rs2650761	0.82[AFR][1000 genomes]
rs2650762	0.82[AFR][1000 genomes]
rs2650765	0.82[AFR][1000 genomes]
rs2650796	0.85[AFR][1000 genomes]
rs2650813	0.82[AFR][1000 genomes]
rs2650815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650818	0.85[AFR][1000 genomes]
rs2650820	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650821	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650823	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2650837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2681397	1.00[AMR][1000 genomes]
rs28580140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28581819	0.82[AFR][1000 genomes]
rs2914653	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2968068	1.00[AMR][1000 genomes]
rs2968077	0.85[AFR][1000 genomes]
rs987772	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	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	chr19:21647000-21657200	Weak transcription	Right Atrium	heart
2	chr19:21653200-21654000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:21653800-21657200	Weak transcription	Placenta Amnion	Placenta Amnion

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