Variant report

Variant	rs56761356
Chromosome Location	chr20:1094892-1094893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:144)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:144 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr20:1094745-1095058	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr20:1094778-1095000	MCF-7	breast:	n/a	n/a
3	CTCF	chr20:1094655-1095123	A549	lung:	n/a	n/a
4	CTCF	chr20:1094661-1095117	HCT-116	colon:	n/a	n/a
5	RAD21	chr20:1094708-1095107	HepG2	liver:	n/a	n/a
6	CTCF	chr20:1094860-1095010	HBMEC	blood vessel:	n/a	n/a
7	JUND	chr20:1094860-1094995	HepG2	liver:	n/a	n/a
8	ELF1	chr20:1094788-1095068	MCF-7	breast:	n/a	n/a
9	CTCF	chr20:1094786-1094970	IMR90	lung:	n/a	n/a
10	MAFF	chr20:1094862-1094976	K562	blood:	n/a	n/a
11	HCFC1	chr20:1094862-1095045	K562	blood:	n/a	n/a
12	CTCF	chr20:1094780-1094930	GM12874	blood:	n/a	n/a
13	SMC3	chr20:1094747-1095084	HepG2	liver:	n/a	n/a
14	RAD21	chr20:1094772-1095007	H1-hESC	embryonic stem cell:	n/a	n/a
15	SMC3	chr20:1094784-1094984	K562	blood:	n/a	n/a
16	STAT1	chr20:1094808-1095231	Hela-S3	cervix:	n/a	chr20:1094991-1095002
17	CTCF	chr20:1094703-1095120	K562	blood:	n/a	n/a
18	CTCF	chr20:1094780-1094930	AG04450	lung:	n/a	n/a
19	CTCF	chr20:1094860-1095010	HEK293	kidney:	n/a	n/a
20	CTCF	chr20:1094800-1094950	BJ	skin:	n/a	n/a
21	CTCF	chr20:1094600-1095143	HCT-116	colon:	n/a	n/a
22	CTCF	chr20:1094831-1094977	ProgFib	skin:	n/a	n/a
23	CTCF	chr20:1094759-1095054	MCF-7	breast:	n/a	n/a
24	CTCF	chr20:1094820-1094970	RPTEC	kidney:	n/a	n/a
25	POLR2A	chr20:1094780-1095272	K562	blood:	n/a	n/a
26	CTCF	chr20:1094777-1094984	GM12878	blood:	n/a	n/a
27	ZNF143	chr20:1094843-1095016	K562	blood:	n/a	n/a
28	CTCF	chr20:1094808-1094948	GM12892	blood:	n/a	n/a
29	CTCF	chr20:1094849-1094968	Fibrobl	skin:	n/a	n/a
30	CTCF	chr20:1094860-1095010	HVMF	connective:	n/a	n/a
31	CTCF	chr20:1094840-1094990	BJ	skin:	n/a	n/a
32	GABPA	chr20:1094877-1095029	K562	blood:	n/a	n/a
33	CTCF	chr20:1094800-1094950	SK-N-SH_RA	brain:	n/a	n/a
34	CTCF	chr20:1094820-1095110	HFF-Myc	foreskin:	n/a	n/a
35	CTCF	chr20:1094840-1094990	HMEC	breast:	n/a	n/a
36	ZNF143	chr20:1094749-1095038	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAZ	chr20:1094789-1095119	K562	blood:	n/a	n/a
38	THAP1	chr20:1094821-1094958	K562	blood:	n/a	n/a
39	POLR2A	chr20:1094837-1094928	HUVEC	blood vessel:	n/a	n/a
40	GABPA	chr20:1094777-1095144	A549	lung:	n/a	n/a
41	CTCF	chr20:1094780-1094930	K562	blood:	n/a	n/a
42	ELF1	chr20:1094733-1095070	K562	blood:	n/a	n/a
43	CTCF	chr20:1094772-1095022	MCF-7	breast:	n/a	n/a
44	CTCF	chr20:1094840-1094990	AG04450	lung:	n/a	n/a
45	CTCF	chr20:1094800-1094950	RPTEC	kidney:	n/a	n/a
46	RAD21	chr20:1094763-1095038	HepG2	liver:	n/a	n/a
47	CTCF	chr20:1094840-1094990	HPAF	blood vessel:	n/a	n/a
48	CTCF	chr20:1094766-1095066	T-47D	breast:	n/a	n/a
49	CTCF	chr20:1094780-1094930	NHEK	skin:	n/a	n/a
50	CTCF	chr20:1094680-1095099	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:796795..797298-chr20:1094428..1094937,2	K562	blood:
2	chr20:1093479..1095284-chr20:1095646..1099615,3	K562	blood:
3	chr20:1094199..1096459-chr20:1097621..1099554,3	MCF-7	breast:

No data

Variant related genes	Relation type
PSMF1	TF binding region
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2092370	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813031	0.96[ASN][1000 genomes]
rs55751955	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074139	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6077755	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6077759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6077768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6077769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6077771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6077773	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6077774	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6077779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6077792	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6104589	0.94[ASN][1000 genomes]
rs6131084	0.96[ASN][1000 genomes]
rs73069840	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS 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
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1085600-1098200	Weak transcription	Spleen	Spleen
2	chr20:1089000-1098200	Weak transcription	K562	blood
3	chr20:1089200-1098200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:1089400-1098200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr20:1089800-1095000	Weak transcription	HepG2	liver
6	chr20:1094000-1097800	Weak transcription	Pancreas	Pancrea
7	chr20:1094600-1095000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr20:1094600-1095000	Enhancers	Fetal Muscle Trunk	muscle
9	chr20:1094600-1095200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr20:1094600-1095200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr20:1094800-1095000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:1094800-1095000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:1094800-1095000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr20:1094800-1095000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:1094800-1095000	Enhancers	Adipose Nuclei	Adipose
16	chr20:1094800-1095000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links