Variant report

Variant	rs59082275
Chromosome Location	chr20:25204137-25204138
allele	A/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	NR2F2	chr20:25203802-25204216	K562	blood:	n/a	n/a
2	POLR2A	chr20:25203196-25204271	HepG2	liver:	n/a	n/a
3	FOSL2	chr20:25203779-25204187	A549	lung:	n/a	chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204008-25204019
4	JUN	chr20:25203762-25204313	K562	blood:	n/a	chr20:25204130-25204143 chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204008-25204019
5	POLR2A	chr20:25203749-25204230	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr20:25204000-25204150	HVMF	connective:	n/a	n/a
7	KAP1	chr20:25203720-25204329	U2OS	brain:	n/a	n/a
8	MYC	chr20:25203363-25204243	NB4	blood:	n/a	chr20:25203652-25203662
9	RAD21	chr20:25203754-25204242	HepG2	liver:	n/a	chr20:25203949-25203962
10	TCF12	chr20:25203678-25204468	A549	lung:	n/a	chr20:25203915-25203925
11	ARID3A	chr20:25203915-25204289	K562	blood:	n/a	n/a
12	MYC	chr20:25203767-25204300	MCF10A-Er-Src	breast:	n/a	n/a
13	MXI1	chr20:25203176-25204426	IMR90	lung:	n/a	n/a
14	FOS	chr20:25203839-25204265	MCF10A-Er-Src	breast:	n/a	chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204005-25204016 chr20:25204008-25204019
15	CTCF	chr20:25203800-25204177	MCF-7	breast:	n/a	chr20:25203945-25203963 chr20:25203948-25203956 chr20:25203947-25203955 chr20:25203948-25203961
16	RAD21	chr20:25203874-25204156	K562	blood:	n/a	chr20:25203949-25203962
17	JUND	chr20:25203827-25204167	HepG2	liver:	n/a	chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204005-25204016 chr20:25204008-25204019
18	MAX	chr20:25203744-25204403	SK-N-SH	brain:	n/a	n/a
19	KAP1	chr20:25203761-25204312	HEK293	kidney:	n/a	n/a
20	MYC	chr20:25203704-25204264	K562	blood:	n/a	n/a
21	POLR2A	chr20:25203853-25204364	K562	blood:	n/a	n/a
22	FOXP2	chr20:25203794-25204196	PFSK-1	brain:	n/a	n/a
23	MAX	chr20:25203818-25204259	A549	lung:	n/a	n/a
24	RAD21	chr20:25203730-25204336	IMR90	lung:	n/a	chr20:25203949-25203962
25	TEAD4	chr20:25203875-25204304	K562	blood:	n/a	n/a
26	POLR2A	chr20:25203860-25204155	MCF10A-Er-Src	breast:	n/a	n/a
27	TCF12	chr20:25203703-25204282	ECC-1	luminal epithelium:	n/a	chr20:25203915-25203925
28	TBL1XR1	chr20:25203866-25204292	K562	blood:	n/a	n/a
29	TAL1	chr20:25203886-25204273	K562	blood:	n/a	n/a
30	TAF1	chr20:25203877-25204179	SK-N-SH	brain:	n/a	n/a
31	JUND	chr20:25203658-25204441	SK-N-SH	brain:	n/a	chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204005-25204016 chr20:25204008-25204019
32	TCF12	chr20:25203623-25204478	SK-N-SH	brain:	n/a	chr20:25203915-25203925 chr20:25203649-25203659
33	POLR2A	chr20:25203725-25204280	HCT-116	colon:	n/a	n/a
34	SP1	chr20:25203637-25204341	HCT-116	colon:	n/a	chr20:25203658-25203667 chr20:25203659-25203668 chr20:25203654-25203668 chr20:25203657-25203669 chr20:25203657-25203669 chr20:25203658-25203668
35	TRIM28	chr20:25203841-25204300	K562	blood:	n/a	n/a
36	UBTF	chr20:25203860-25204263	K562	blood:	n/a	n/a
37	RAD21	chr20:25203646-25204213	MCF-7	breast:	n/a	chr20:25203949-25203962 chr20:25203655-25203665
38	CEBPD	chr20:25203875-25204387	K562	blood:	n/a	n/a
39	ZMIZ1	chr20:25203821-25204246	K562	blood:	n/a	n/a
40	ZC3H11A	chr20:25203819-25204254	K562	blood:	n/a	n/a
41	REST	chr20:25203860-25204166	SK-N-SH	brain:	n/a	n/a
42	SP1	chr20:25203673-25204333	A549	lung:	n/a	n/a
43	REST	chr20:25203675-25204357	A549	lung:	n/a	n/a
44	BACH1	chr20:25203904-25204319	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr20:25203684-25204411	A549	lung:	n/a	chr20:25203949-25203962
46	ELF1	chr20:25203715-25204238	K562	blood:	n/a	n/a
47	RAD21	chr20:25203722-25204299	A549	lung:	n/a	chr20:25203949-25203962
48	RAD21	chr20:25203815-25204222	SK-N-SH_RA	brain:	n/a	chr20:25203949-25203962
49	MAX	chr20:25203368-25204269	NB4	blood:	n/a	chr20:25203652-25203662
50	JUND	chr20:25203751-25204351	K562	blood:	n/a	chr20:25204005-25204017 chr20:25204007-25204015 chr20:25204005-25204016 chr20:25204008-25204019

No.	Distal block	Cell Line	Cell type
1	chr20:25200007..25207026-chr20:25227086..25230373,11	MCF-7	breast:
2	chr20:25203499..25204385-chr20:25227516..25228200,3	MCF-7	breast:
3	chr20:25202638..25204981-chr20:25290392..25292529,2	MCF-7	breast:
4	chr20:25204037..25205721-chr20:25227160..25229400,2	K562	blood:
5	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
6	chr20:25202506..25206898-chr20:25226343..25231297,7	MCF-7	breast:

Variant related genes	Relation type
ENTPD6	TF binding region
ENSG00000197586	Chromatin interaction
ENSG00000100997	Chromatin interaction
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11907515	0.83[EUR][1000 genomes]
rs11907597	0.83[AMR][1000 genomes]
rs2067793	0.83[EUR][1000 genomes]
rs2145125	0.83[EUR][1000 genomes]
rs2180596	0.83[EUR][1000 genomes]
rs2180597	0.83[EUR][1000 genomes]
rs2228978	0.83[EUR][1000 genomes]
rs2387734	0.83[EUR][1000 genomes]
rs28496800	0.83[EUR][1000 genomes]
rs28770021	0.83[EUR][1000 genomes]
rs28881233	0.83[EUR][1000 genomes]
rs34299454	0.83[EUR][1000 genomes]
rs41282340	0.83[EUR][1000 genomes]
rs41304802	0.83[EUR][1000 genomes]
rs41308633	0.83[EUR][1000 genomes]
rs57405931	0.83[EUR][1000 genomes]
rs58412968	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58953621	1.00[EUR][1000 genomes]
rs6037061	0.83[EUR][1000 genomes]
rs6037064	0.83[EUR][1000 genomes]
rs6037068	0.83[EUR][1000 genomes]
rs6037070	0.83[EUR][1000 genomes]
rs6037071	0.83[EUR][1000 genomes]
rs6037073	0.83[EUR][1000 genomes]
rs6037075	0.83[EUR][1000 genomes]
rs6050449	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6050451	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6050457	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6050458	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6050461	0.83[EUR][1000 genomes]
rs6050462	0.83[EUR][1000 genomes]
rs6050465	0.83[EUR][1000 genomes]
rs6050473	0.83[EUR][1000 genomes]
rs6050474	0.83[EUR][1000 genomes]
rs6050476	0.83[EUR][1000 genomes]
rs6050478	0.83[EUR][1000 genomes]
rs6050486	0.83[EUR][1000 genomes]
rs6050487	0.83[EUR][1000 genomes]
rs6050488	0.83[EUR][1000 genomes]
rs6050490	0.83[EUR][1000 genomes]
rs6050492	0.83[EUR][1000 genomes]
rs6050493	0.83[EUR][1000 genomes]
rs6050494	0.83[EUR][1000 genomes]
rs6050502	0.83[EUR][1000 genomes]
rs6050503	0.83[EUR][1000 genomes]
rs6050504	0.83[EUR][1000 genomes]
rs6050507	0.83[EUR][1000 genomes]
rs6050508	0.83[EUR][1000 genomes]
rs6050509	0.83[EUR][1000 genomes]
rs6050510	0.83[EUR][1000 genomes]
rs6050511	0.83[EUR][1000 genomes]
rs7263527	0.83[EUR][1000 genomes]
rs7269045	0.83[EUR][1000 genomes]
rs7270324	0.83[EUR][1000 genomes]
rs7273544	0.83[EUR][1000 genomes]
rs7274919	1.00[EUR][1000 genomes]
rs73343076	1.00[EUR][1000 genomes]
rs73347016	1.00[EUR][1000 genomes]
rs73347066	1.00[EUR][1000 genomes]
rs7344105	0.83[EUR][1000 genomes]
rs736358	0.83[EUR][1000 genomes]
rs8116564	0.83[EUR][1000 genomes]
rs8118763	0.83[EUR][1000 genomes]
rs8120268	0.83[EUR][1000 genomes]
rs8123947	1.00[EUR][1000 genomes]
rs8125980	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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 target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr20:25190400-25205200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:25190400-25207200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr20:25190400-25207200	Strong transcription	Fetal Stomach	stomach
7	chr20:25190400-25207200	Strong transcription	Ovary	ovary
8	chr20:25190600-25207000	Strong transcription	Fetal Brain Female	brain
9	chr20:25190600-25207200	Strong transcription	Brain Germinal Matrix	brain
10	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
11	chr20:25191600-25204200	Strong transcription	Brain Angular Gyrus	brain
12	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
14	chr20:25197200-25208000	Weak transcription	Primary B cells from cord blood	blood
15	chr20:25197400-25207400	Weak transcription	Fetal Brain Male	brain
16	chr20:25197400-25207400	Weak transcription	NHDF-Ad	bronchial
17	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
18	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
19	chr20:25198800-25207200	Genic enhancers	Right Ventricle	heart
20	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:25199200-25207400	Weak transcription	Psoas Muscle	Psoas
22	chr20:25199200-25208600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr20:25199600-25206000	Weak transcription	Aorta	Aorta
27	chr20:25200000-25204400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr20:25200200-25204200	Genic enhancers	Fetal Muscle Leg	muscle
29	chr20:25200200-25207400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:25201000-25204800	Enhancers	Left Ventricle	heart
31	chr20:25201200-25204400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr20:25201200-25207400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr20:25201600-25204400	Weak transcription	Colonic Mucosa	Colon
34	chr20:25201600-25208200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:25201800-25205600	Strong transcription	Pancreas	Pancrea
36	chr20:25201800-25205800	Weak transcription	Brain Substantia Nigra	brain
37	chr20:25201800-25207000	Strong transcription	Lung	lung
38	chr20:25202000-25204400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:25202000-25205200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr20:25202000-25207200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr20:25202200-25207400	Weak transcription	Colon Smooth Muscle	Colon
42	chr20:25202200-25209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr20:25202400-25204400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr20:25202400-25204400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr20:25202400-25206000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr20:25202400-25206400	Weak transcription	Liver	Liver
47	chr20:25202600-25205400	Enhancers	NH-A	brain
48	chr20:25202800-25204200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:25202800-25204400	Genic enhancers	Fetal Intestine Small	intestine
50	chr20:25202800-25204400	Weak transcription	Placenta	Placenta

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