Variant report

Variant	rs56175611
Chromosome Location	chr2:20425812-20425813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20425661-20425950	HepG2	liver:	n/a	n/a
2	RAD21	chr2:20420269-20426598	SK-N-SH	brain:	n/a	chr2:20422198-20422210 chr2:20424162-20424172 chr2:20425226-20425238 chr2:20423347-20423361
3	NFIC	chr2:20424972-20426031	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:20424950-20425955	HepG2	liver:	n/a	n/a
5	ESRRA	chr2:20424274-20426108	GM12878	blood:	n/a	chr2:20425299-20425312 chr2:20425885-20425901
6	ZNF263	chr2:20424394-20426249	HEK293-T-REx	kidney:	n/a	n/a
7	HNF4G	chr2:20425019-20425976	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
8	YY1	chr2:20425738-20425894	K562	blood:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
9	MAX	chr2:20422503-20426249	HepG2	liver:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
10	POLR2A	chr2:20422936-20425902	MCF-7	breast:	n/a	n/a
11	RAD21	chr2:20424784-20425815	HCT-116	colon:	n/a	chr2:20425226-20425238
12	ZNF143	chr2:20425130-20425846	H1-hESC	embryonic stem cell:	n/a	n/a
13	NR2F2	chr2:20424957-20426048	MCF-7	breast:	n/a	n/a
14	HNF4A	chr2:20425581-20425947	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
15	YY1	chr2:20425564-20426061	HepG2	liver:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
16	GTF2F1	chr2:20425270-20425831	H1-hESC	embryonic stem cell:	n/a	n/a
17	HDAC2	chr2:20422965-20425963	HepG2	liver:	n/a	n/a
18	MYBL2	chr2:20424962-20425949	HepG2	liver:	n/a	n/a
19	MAX	chr2:20424253-20425899	MCF-7	breast:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
20	MAX	chr2:20423554-20425885	ECC-1	luminal epithelium:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
21	YY1	chr2:20425465-20426067	H1-hESC	embryonic stem cell:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
22	TBP	chr2:20424795-20425858	H1-hESC	embryonic stem cell:	n/a	n/a
23	HEY1	chr2:20425563-20425973	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:20424943-20425987	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYBL2	chr2:20424431-20426143	HepG2	liver:	n/a	n/a
26	MAX	chr2:20422708-20425903	A549	lung:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
27	E2F6	chr2:20425771-20425911	K562	blood:	n/a	n/a
28	YY1	chr2:20425668-20426006	GM12891	blood:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
29	POLR2A	chr2:20422475-20425920	HepG2	liver:	n/a	n/a
30	HNF4A	chr2:20425072-20426030	HepG2	liver:	n/a	chr2:20425988-20425996 chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
31	MAX	chr2:20424979-20426145	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr2:20424981-20426097	H1-hESC	embryonic stem cell:	n/a	chr2:20425402-20425411
33	BCL3	chr2:20424576-20425814	A549	lung:	n/a	chr2:20424952-20424965 chr2:20425487-20425500 chr2:20424671-20424684 chr2:20424655-20424668 chr2:20425064-20425072
34	MAX	chr2:20422574-20426033	A549	lung:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
35	POLR2A	chr2:20424988-20425822	H1-hESC	embryonic stem cell:	n/a	n/a
36	MBD4	chr2:20424987-20426304	HepG2	liver:	n/a	n/a
37	HNF4A	chr2:20425597-20425939	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
38	MAX	chr2:20424310-20425897	HepG2	liver:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
39	MAX	chr2:20424290-20426109	H1-hESC	embryonic stem cell:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
40	E2F6	chr2:20424130-20426019	A549	lung:	n/a	chr2:20424518-20424533 chr2:20425402-20425411 chr2:20424825-20424840 chr2:20424641-20424653 chr2:20424639-20424649 chr2:20424952-20424961 chr2:20424522-20424534
41	YY1	chr2:20425023-20426205	H1-hESC	embryonic stem cell:	n/a	chr2:20425836-20425844 chr2:20425825-20425847 chr2:20425301-20425312
42	HEY1	chr2:20424970-20425950	HepG2	liver:	n/a	n/a
43	TCF12	chr2:20422666-20425889	A549	lung:	n/a	chr2:20423285-20423292 chr2:20424751-20424761 chr2:20423418-20423425 chr2:20424823-20424830
44	ELF1	chr2:20425674-20425959	HepG2	liver:	n/a	chr2:20425915-20425926
45	SMC3	chr2:20420380-20425872	SK-N-SH	brain:	n/a	chr2:20424162-20424172
46	HCFC1	chr2:20423412-20425864	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr2:20425784-20425826	MCF-7	breast:	n/a	n/a
48	MAX	chr2:20422517-20426010	HCT-116	colon:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
49	CTCF	chr2:20421105-20426546	SK-N-SH	brain:	n/a	chr2:20425315-20425325 chr2:20423923-20423936
50	YY1	chr2:20424958-20426180	HepG2	liver:	n/a	chr2:20425836-20425844 chr2:20425825-20425847 chr2:20425301-20425312

No.	Distal block	Cell Line	Cell type
1	chr2:20299695..20307724-chr2:20421846..20426859,15	MCF-7	breast:
2	chr2:20425705..20426396-chr2:20447809..20448700,2	MCF-7	breast:
3	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
4	chr2:20422608..20425941-chr2:20442995..20447318,5	MCF-7	breast:
5	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:
6	chr2:20097107..20100415-chr2:20424161..20425989,3	K562	blood:
7	chr2:20421499..20423791-chr2:20425335..20427623,2	K562	blood:

Variant related genes	Relation type
SDC1	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000238735	Chromatin interaction
ENSG00000234378	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000223734	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13383113	0.89[AMR][1000 genomes]
rs34057700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56021041	0.89[AMR][1000 genomes]
rs57753286	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61039314	0.89[AMR][1000 genomes]
rs73214387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73216297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73216299	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73218109	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73218119	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73218120	0.86[AFR][1000 genomes]
rs73231458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73231460	1.00[AFR][1000 genomes];1.00[AMR][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	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3398925	chr2:20423871-20426119	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20422800-20426000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:20425200-20426000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:20425200-20426000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:20425200-20426000	Enhancers	Lung	lung
5	chr2:20425200-20426200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:20425200-20426200	Flanking Active TSS	Colonic Mucosa	Colon
7	chr2:20425400-20426000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr2:20425400-20426000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:20425400-20426000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr2:20425400-20426000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:20425400-20426000	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr2:20425400-20426000	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr2:20425400-20426200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:20425400-20426200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:20425400-20426200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:20425400-20426200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:20425400-20426200	Flanking Active TSS	Liver	Liver
18	chr2:20425400-20426200	Enhancers	Gastric	stomach
19	chr2:20425400-20426200	Enhancers	Pancreas	Pancrea
20	chr2:20425400-20426200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:20425400-20426200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:20425400-20426200	Flanking Active TSS	HepG2	liver
23	chr2:20425600-20426000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:20425600-20426000	Enhancers	Primary B cells from cord blood	blood
25	chr2:20425600-20426000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr2:20425600-20426000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr2:20425600-20426000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:20425600-20426000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:20425600-20426000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:20425600-20426000	Bivalent Enhancer	Fetal Thymus	thymus
31	chr2:20425600-20426000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr2:20425600-20426200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr2:20425600-20426200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:20425600-20426200	Enhancers	Fetal Lung	lung
35	chr2:20425600-20426200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:20425600-20426200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr2:20425600-20426400	Bivalent Enhancer	Placenta	Placenta
38	chr2:20425600-20426400	Enhancers	Stomach Mucosa	stomach
39	chr2:20425600-20427800	Weak transcription	Osteobl	bone
40	chr2:20425600-20429400	Weak transcription	NHDF-Ad	bronchial
41	chr2:20425600-20429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:20425800-20426000	Enhancers	Primary hematopoietic stem cells	blood
43	chr2:20425800-20426000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:20425800-20426000	Bivalent Enhancer	Adipose Nuclei	Adipose
45	chr2:20425800-20426000	Enhancers	GM12878-XiMat	blood
46	chr2:20425800-20426000	Enhancers	Hela-S3	cervix
47	chr2:20425800-20426200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
48	chr2:20425800-20426200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
49	chr2:20425800-20426200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr2:20425800-20426200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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