Variant report

Variant	rs6132864
Chromosome Location	chr20:25737388-25737389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs35016365	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35364051	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6115241	0.81[CEU][hapmap]
rs6132857	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132858	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132861	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132862	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132863	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138601	1.00[CEU][hapmap]
rs6138604	0.93[CEU][hapmap]
rs6138616	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6138622	0.83[EUR][1000 genomes]
rs6138623	0.83[EUR][1000 genomes]
rs6138625	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138631	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138633	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138639	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138643	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138647	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138650	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6138653	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138659	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
5	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1062442	chr20:25714010-25754838	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	esv18917	chr20:25731048-25780918	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv820681	chr20:25731048-25780918	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv979422	chr20:25732656-25867609	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv962599	chr20:25735409-25754388	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS	lncRNA	n/a	inside rSNPs	diseases
12	esv3336992	chr20:25735952-25759650	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3330678	chr20:25735952-25760550	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3427819	chr20:25735952-25760550	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3429256	chr20:25735952-25770050	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv3352879	chr20:25736052-25753750	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	lncRNA	n/a	inside rSNPs	diseases
17	esv3454794	chr20:25737235-25738070	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
18	esv3454795	chr20:25737249-25738062	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6132864	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6132864	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6132864	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6132864	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6132864	PYGB	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25732200-25737800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:25732400-25737800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:25732600-25737800	Weak transcription	Thymus	Thymus

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