Variant report

Variant	rs61338465
Chromosome Location	chr20:52784588-52784589
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	YY1	chr20:52784375-52784604	HCT-116	colon:	n/a	n/a
2	NFIC	chr20:52784335-52785158	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr20:52784307-52785208	A549	lung:	n/a	n/a
4	TCF7L2	chr20:52784420-52785174	HCT-116	colon:	n/a	n/a
5	SP1	chr20:52781349-52785310	A549	lung:	n/a	n/a
6	ETS1	chr20:52784518-52784929	A549	lung:	n/a	n/a
7	SP1	chr20:52784310-52785318	A549	lung:	n/a	n/a
8	SIN3AK20	chr20:52783388-52785190	A549	lung:	n/a	n/a
9	USF1	chr20:52782018-52785212	A549	lung:	n/a	n/a
10	POLR2A	chr20:52784526-52784814	A549	lung:	n/a	n/a
11	ZBTB33	chr20:52784306-52785207	A549	lung:	n/a	n/a
12	SIN3AK20	chr20:52784327-52785243	A549	lung:	n/a	n/a
13	REST	chr20:52783230-52785235	A549	lung:	n/a	chr20:52784756-52784765
14	POLR2A	chr20:52784423-52785103	HCT-116	colon:	n/a	n/a
15	CEBPB	chr20:52784282-52785144	A549	lung:	n/a	n/a
16	FOSL2	chr20:52784224-52785336	A549	lung:	n/a	n/a
17	YY1	chr20:52784320-52785127	A549	lung:	n/a	n/a
18	SP1	chr20:52784283-52785186	HCT-116	colon:	n/a	n/a
19	ATF3	chr20:52784248-52785237	A549	lung:	n/a	n/a
20	E2F4	chr20:52784164-52785029	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr20:52784501-52785059	A549	lung:	n/a	n/a
22	GATA3	chr20:52776064-52785298	A549	lung:	n/a	chr20:52778354-52778363 chr20:52778722-52778732 chr20:52778722-52778731 chr20:52776796-52776806 chr20:52779429-52779436
23	FOS	chr20:52784389-52785120	MCF10A-Er-Src	breast:	n/a	n/a
24	TAF1	chr20:52784355-52785231	A549	lung:	n/a	n/a
25	POLR2A	chr20:52784355-52785218	HCT-116	colon:	n/a	n/a
26	POLR2A	chr20:52784377-52784709	ProgFib	skin:	n/a	n/a
27	MAX	chr20:52784255-52785350	A549	lung:	n/a	n/a
28	POLR2A	chr20:52784343-52785163	A549	lung:	n/a	n/a
29	NFIC	chr20:52784343-52785103	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr20:52772200-52791801	A549	lung:	n/a	chr20:52790233-52790240 chr20:52786044-52786053 chr20:52779960-52779969 chr20:52790231-52790241
31	STAT3	chr20:52784386-52785036	MCF10A-Er-Src	breast:	n/a	n/a
32	ZBTB33	chr20:52784302-52785142	A549	lung:	n/a	n/a
33	POLR2A	chr20:52784370-52785157	A549	lung:	n/a	n/a
34	POLR2A	chr20:52770188-52790693	A549	lung:	n/a	n/a
35	FOS	chr20:52784367-52785120	MCF10A-Er-Src	breast:	n/a	n/a
36	MYC	chr20:52784402-52785058	MCF10A-Er-Src	breast:	n/a	n/a
37	BCL3	chr20:52772170-52791941	A549	lung:	n/a	chr20:52790491-52790504 chr20:52782584-52782593 chr20:52784755-52784763 chr20:52790858-52790871 chr20:52790857-52790870 chr20:52782583-52782592
38	MYC	chr20:52784451-52785059	MCF10A-Er-Src	breast:	n/a	n/a
39	ELF1	chr20:52783507-52785252	A549	lung:	n/a	n/a
40	STAT3	chr20:52784423-52785085	MCF10A-Er-Src	breast:	n/a	n/a
41	NFIC	chr20:52784290-52784777	ECC-1	luminal epithelium:	n/a	n/a
42	JUND	chr20:52784395-52785208	A549	lung:	n/a	n/a
43	MAX	chr20:52784323-52785267	HCT-116	colon:	n/a	n/a
44	MAX	chr20:52784300-52785307	HCT-116	colon:	n/a	n/a
45	EP300	chr20:52782097-52785248	A549	lung:	n/a	chr20:52783664-52783674 chr20:52782863-52782877 chr20:52782584-52782593 chr20:52782583-52782592
46	JUND	chr20:52783667-52785166	A549	lung:	n/a	n/a
47	ATF3	chr20:52784334-52785014	A549	lung:	n/a	n/a
48	TEAD4	chr20:52784325-52785189	A549	lung:	n/a	n/a
49	TCF7L2	chr20:52784509-52784614	Hela-S3	cervix:	n/a	n/a
50	PBX3	chr20:52784194-52785328	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:56728473..56731849-chr20:52782841..52785983,3	MCF-7	breast:
2	chr17:56735532..56737839-chr20:52784476..52786335,2	MCF-7	breast:
3	chr20:45985630..45987626-chr20:52781307..52785210,3	MCF-7	breast:
4	chr20:52784538..52787745-chr20:55839134..55841996,3	MCF-7	breast:
5	chr20:52765302..52766219-chr20:52784081..52784986,2	MCF-7	breast:
6	chr17:57920588..57922273-chr20:52783196..52786191,2	MCF-7	breast:
7	chr20:52784393..52784975-chr20:52811607..52812127,2	MCF-7	breast:

Variant related genes	Relation type
CYP24A1	TF binding region
ENSG00000226308	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6022993	1.00[AMR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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 miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv3449693	chr20:52784550-52785027	Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:52777800-52784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:52778800-52784600	Weak transcription	HepG2	liver
7	chr20:52784200-52786200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:52784200-52786200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52784400-52784600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:52784400-52784600	Bivalent Enhancer	Osteobl	bone
11	chr20:52784400-52785200	Enhancers	HMEC	breast
12	chr20:52784400-52786400	Enhancers	NHEK	skin

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