Variant report

Variant	rs56099949
Chromosome Location	chr3:20053948-20053949
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:20053764-20053964	K562	blood:	n/a	chr3:20053812-20053823

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20053940-20053990	AoSMC	blood vessel:	n/a
2	chr3:20053940-20053990	HUVEC	blood vessel:	n/a
3	chr3:20053940-20053990	RPTEC	kidney:	n/a
4	chr3:20053940-20053990	GM12878	blood:	n/a
5	chr3:20053940-20053990	NH-A	brain:	n/a
6	chr3:20053940-20053990	HCT-116	colon:	n/a
7	chr3:20053940-20053990	AG04450	lung:	fetal
8	chr3:20053940-20053990	CMK	blood:	n/a
9	chr3:20053940-20053990	HEK293	kidney:	embryo
10	chr3:20053940-20053990	ProgFib	skin:	n/a
11	chr3:20053940-20053990	NHBE	bronchial:	n/a
12	chr3:20053940-20053990	U87	brain:	n/a
13	chr3:20053940-20053990	SKMC	muscle:	n/a
14	chr3:20053940-20053990	SK-N-MC	brain:	n/a
15	chr3:20053940-20053990	HRE	kidney:	n/a
16	chr3:20053940-20053990	HRCEpiC	kidney:	n/a
17	chr3:20053940-20053990	H1-hESC	embryonic stem cell:	embryo
18	chr3:20053940-20053990	HAEpiC	amniotic membrane:	n/a
19	chr3:20053940-20053990	SK-N-SH_RA	brain:	n/a
20	chr3:20053940-20053990	HNPCEpiC	eye:	n/a
21	chr3:20053940-20053990	PANC-1	pancreas:	n/a
22	chr3:20053940-20053990	Caco-2	colon:	n/a
23	chr3:20053940-20053990	HRPEpiC	eye:	n/a
24	chr3:20053940-20053990	BE2_C	brain:	n/a
25	chr3:20053940-20053990	Hela-S3	cervix:	n/a
26	chr3:20053940-20053990	Jurkat	blood:	n/a
27	chr3:20053940-20053990	HPAEpiC	pulmonary alveolar:	n/a
28	chr3:20053940-20053990	GM12892	blood:	n/a
29	chr3:20053940-20053990	PFSK-1	brain:	n/a
30	chr3:20053940-20053990	HCF	heart:	n/a
31	chr3:20053940-20053990	HEEpiC	esophagus:	n/a
32	chr3:20053940-20053990	GM12891	blood:	n/a
33	chr3:20053940-20053990	K562	blood:	n/a
34	chr3:20053940-20053990	ECC-1	luminal epithelium:	n/a
35	chr3:20053940-20053990	Hepatocyte	liver:	n/a
36	chr3:20053940-20053990	HIPEpiC	eye:	n/a
37	chr3:20053940-20053990	NT2-D1	testis:	n/a
38	chr3:20053940-20053990	SAEC	small airway:	n/a
39	chr3:20053940-20053990	IMR90	lung:	fetal
40	chr3:20053940-20053990	SK-N-SH	brain:	n/a
41	chr3:20053940-20053990	HCM	heart:	n/a
42	chr3:20053940-20053990	LNCaP	prostate:	n/a
43	chr3:20053940-20053990	HepG2	liver:	n/a
44	chr3:20053940-20053990	HCPEpiC	choroid plexus:	n/a
45	chr3:20053940-20053990	AG09309	skin:	n/a
46	chr3:20053940-20053990	A549	lung:	n/a
47	chr3:20053940-20053990	NB4	blood:	n/a
48	chr3:20053940-20053990	AG04449	skin:	fetal
49	chr3:20053940-20053990	NHDF-neo	bronchial:	n/a
50	chr3:20053940-20053990	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:20046912..20049769-chr3:20052524..20055370,2	K562	blood:
2	chr3:19991110..19993492-chr3:20053410..20056377,2	K562	blood:
3	chr3:20053872..20056558-chr3:20225792..20227888,2	K562	blood:

No data

Variant related genes	Relation type
PP2D1	TF binding region
ENSG00000230697	TF binding region
ENSG00000230697	CpG island
PP2D1	CpG island
ENSG00000129810	Chromatin interaction
ENSG00000230697	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1133442	0.93[EUR][1000 genomes]
rs62241332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73034128	0.87[AMR][1000 genomes];0.93[EUR][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	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
11	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv979809	chr3:20052873-20056586	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20052000-20056400	Weak transcription	Right Atrium	heart
2	chr3:20053600-20058000	Enhancers	K562	blood

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