Variant report

Variant	rs3004122
Chromosome Location	chr20:23512774-23512775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1155362	1.00[EUR][1000 genomes]
rs1157263	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12625187	1.00[CEU][hapmap]
rs13433149	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1555356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1555358	1.00[EUR][1000 genomes]
rs1555359	0.94[EUR][1000 genomes]
rs2236024	1.00[CEU][hapmap]
rs238645	0.83[ASW][hapmap]
rs2983620	1.00[EUR][1000 genomes]
rs2983624	1.00[CEU][hapmap]
rs2983633	0.94[EUR][1000 genomes]
rs2983645	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3004125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3761278	1.00[CEU][hapmap]
rs60116905	0.94[EUR][1000 genomes]
rs6048848	0.97[EUR][1000 genomes]
rs6048853	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6048856	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6083140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6106675	1.00[EUR][1000 genomes]
rs6106680	1.00[EUR][1000 genomes]
rs6114154	0.87[EUR][1000 genomes]
rs6114159	1.00[CEU][hapmap]
rs6114160	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6114166	1.00[EUR][1000 genomes]
rs6114167	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6114171	0.97[EUR][1000 genomes]
rs7266535	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs911125	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1057992	chr20:23430887-23565333	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv544215	chr20:23430887-23565333	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23510600-23512800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr20:23510800-23513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr20:23511200-23513200	Enhancers	GM12878-XiMat	blood
4	chr20:23512400-23513400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr20:23512400-23513400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr20:23512400-23514200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:23512600-23514200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr20:23512600-23514800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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