Variant report

Variant	rs56157240
Chromosome Location	chr20:25059381-25059382
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25059364-25059414	HL-60	blood:	n/a
2	chr20:25059364-25059414	GM06990	blood:	n/a
3	chr20:25059364-25059414	HRPEpiC	eye:	n/a
4	chr20:25059364-25059414	HEK293	kidney:	embryo
5	chr20:25059364-25059414	PFSK-1	brain:	n/a
6	chr20:25059364-25059414	PANC-1	pancreas:	n/a
7	chr20:25059364-25059414	Caco-2	colon:	n/a
8	chr20:25059364-25059414	HCF	heart:	n/a
9	chr20:25059364-25059414	AG09319	gingival:	n/a
10	chr20:25059364-25059414	H1-hESC	embryonic stem cell:	embryo
11	chr20:25059364-25059414	NHDF-neo	bronchial:	n/a
12	chr20:25059364-25059414	A549	lung:	n/a
13	chr20:25059364-25059414	Hela-S3	cervix:	n/a
14	chr20:25059364-25059414	MCF10A-Er-Src	breast:	n/a
15	chr20:25059364-25059414	HRE	kidney:	n/a
16	chr20:25059364-25059414	HRCEpiC	kidney:	n/a
17	chr20:25059364-25059414	K562	blood:	n/a
18	chr20:25059364-25059414	AG04449	skin:	fetal
19	chr20:25059364-25059414	SK-N-SH_RA	brain:	n/a
20	chr20:25059364-25059414	IMR90	lung:	fetal
21	chr20:25059364-25059414	NT2-D1	testis:	n/a
22	chr20:25059364-25059414	SAEC	small airway:	n/a
23	chr20:25059364-25059414	HAEpiC	amniotic membrane:	n/a
24	chr20:25059364-25059414	HCPEpiC	choroid plexus:	n/a
25	chr20:25059364-25059414	NH-A	brain:	n/a
26	chr20:25059364-25059414	BE2_C	brain:	n/a
27	chr20:25059364-25059414	Hepatocyte	liver:	n/a
28	chr20:25059364-25059414	BJ	skin:	n/a
29	chr20:25059364-25059414	SK-N-SH	brain:	n/a
30	chr20:25059364-25059414	MCF-7	breast:	n/a
31	chr20:25059364-25059414	AoSMC	blood vessel:	n/a
32	chr20:25059364-25059414	GM12878	blood:	n/a
33	chr20:25059364-25059414	U87	brain:	n/a
34	chr20:25059364-25059414	HPAEpiC	pulmonary alveolar:	n/a
35	chr20:25059364-25059414	AG04450	lung:	fetal
36	chr20:25059364-25059414	HCT-116	colon:	n/a
37	chr20:25059364-25059414	SK-N-MC	brain:	n/a
38	chr20:25059364-25059414	HIPEpiC	eye:	n/a
39	chr20:25059364-25059414	ProgFib	skin:	n/a
40	chr20:25059364-25059414	GM12892	blood:	n/a
41	chr20:25059364-25059414	ECC-1	luminal epithelium:	n/a
42	chr20:25059364-25059414	HUVEC	blood vessel:	n/a
43	chr20:25059364-25059414	HNPCEpiC	eye:	n/a
44	chr20:25059364-25059414	HEEpiC	esophagus:	n/a
45	chr20:25059364-25059414	HCM	heart:	n/a
46	chr20:25059364-25059414	AG09309	skin:	n/a
47	chr20:25059364-25059414	ovcar-3	ovarian:	n/a
48	chr20:25059364-25059414	HMEC	breast:	n/a
49	chr20:25059364-25059414	LNCaP	prostate:	n/a
50	chr20:25059364-25059414	T-47D	breast:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25058836..25060785-chr20:25065657..25068597,2	K562	blood:

No data

Variant related genes	Relation type
VSX1	CpG island

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[ASN][1000 genomes]
rs7344824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3345812	chr20:25059286-25059573	Bivalent Enhancer Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25057200-25060600	Enhancers	Dnd41	blood
2	chr20:25058800-25059400	Weak transcription	Colonic Mucosa	Colon
3	chr20:25058800-25061800	Weak transcription	Pancreas	Pancrea

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