Variant report

Variant	rs9880056
Chromosome Location	chr3:53934986-53934987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53930548..53932140-chr3:53934044..53936810,2	K562	blood:
2	chr3:53914533..53916130-chr3:53934096..53936406,2	K562	blood:

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1134091	0.90[EUR][1000 genomes]
rs12632292	0.98[EUR][1000 genomes]
rs17053568	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17053590	1.00[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs1982171	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241806	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs2276840	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276843	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276844	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276845	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289203	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs2304575	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304576	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2884631	0.86[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3733079	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733083	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821868	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821869	0.84[CEU][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41292476	0.88[EUR][1000 genomes]
rs4141606	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45511795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4687753	0.84[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687756	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687760	0.88[EUR][1000 genomes]
rs55917919	0.93[EUR][1000 genomes]
rs56743403	0.91[EUR][1000 genomes]
rs57398949	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253003	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253004	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709324	0.86[EUR][1000 genomes]
rs73078007	0.85[EUR][1000 genomes]
rs9840445	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9849951	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850063	0.98[EUR][1000 genomes]
rs9860367	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs999515	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1005411	chr3:53927782-54158638	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9880056	IL17RB	cis	parietal	SCAN
rs9880056	SFMBT1	cis	cerebellum	SCAN
rs9880056	PHF7	cis	cerebellum	SCAN
rs9880056	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs9880056	ACTR8	cis	parietal	SCAN
rs9880056	ACTR8	cis	lymphoblastoid	seeQTL
rs9880056	IL17RB	cis	Cerebellum	GTEx
rs9880056	ACTR8	cis	cerebellum	SCAN
rs9880056	IL17RB	cis	cerebellum	SCAN
rs9880056	ACTR8	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53933600-53935800	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr3:53934000-53935200	Enhancers	Rectal Mucosa Donor 29	rectum

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