Variant report

Variant	rs58412968
Chromosome Location	chr20:25201021-25201022
allele	A/G
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	CEBPB	chr20:25200626-25201104	HepG2	liver:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200804-25200817
2	MYC	chr20:25200888-25201058	K562	blood:	n/a	n/a
3	CTCF	chr20:25200981-25201094	ProgFib	skin:	n/a	n/a
4	CTCF	chr20:25200920-25201070	AG09319	gingival:	n/a	n/a
5	CTCF	chr20:25200983-25201053	Pancreas_OC	pancreas:	n/a	n/a
6	CTCF	chr20:25201000-25201150	HEK293	kidney:	n/a	n/a
7	CEBPB	chr20:25200503-25201121	A549	lung:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200608-25200616 chr20:25200804-25200817
8	CTCF	chr20:25200820-25201232	K562	blood:	n/a	n/a
9	CTCF	chr20:25200857-25201201	GM12878	blood:	n/a	n/a
10	CTCF	chr20:25200940-25201090	HRPEpiC	eye:	n/a	n/a
11	ZBTB7A	chr20:25200987-25201112	K562	blood:	n/a	n/a
12	CEBPB	chr20:25200616-25201035	HepG2	liver:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200804-25200817
13	CTCF	chr20:25200777-25201131	HepG2	liver:	n/a	n/a
14	CTCF	chr20:25200920-25201070	WI-38	lung:	n/a	n/a
15	CTCF	chr20:25200920-25201070	HEK293	kidney:	n/a	n/a
16	CTCF	chr20:25200948-25201122	Medullo	brain:	n/a	n/a
17	CTCF	chr20:25201000-25201150	GM12867	blood:	n/a	n/a
18	CTCF	chr20:25200912-25201116	MCF-7	breast:	n/a	n/a
19	CTCF	chr20:25200956-25201099	A549	lung:	n/a	n/a
20	CTCF	chr20:25200980-25201130	AG10803	skin:	n/a	n/a
21	CTCF	chr20:25200933-25201104	GM12892	blood:	n/a	n/a
22	CTCF	chr20:25200980-25201130	WERI-Rb-1	eye:	n/a	n/a
23	CTCF	chr20:25201000-25201150	GM12866	blood:	n/a	n/a
24	CTCF	chr20:25200944-25201097	GM10248	blood:	n/a	n/a
25	CTCF	chr20:25200960-25201110	GM12872	blood:	n/a	n/a
26	CTCF	chr20:25201008-25201068	LNCaP	prostate:	n/a	n/a
27	CTCF	chr20:25200980-25201130	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr20:25201000-25201150	BJ	skin:	n/a	n/a
29	CTCF	chr20:25200450-25201319	A549	lung:	n/a	n/a
30	CEBPB	chr20:25200537-25201067	HepG2	liver:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200608-25200616 chr20:25200804-25200817
31	CTCF	chr20:25200940-25201090	GM12868	blood:	n/a	n/a
32	RAD21	chr20:25200918-25201105	SK-N-SH_RA	brain:	n/a	n/a
33	MYC	chr20:25200987-25201079	K562	blood:	n/a	n/a
34	CTCF	chr20:25200920-25201070	HCPEpiC	choroid plexus:	n/a	n/a
35	CEBPB	chr20:25200622-25201164	Hela-S3	cervix:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200804-25200817
36	CTCF	chr20:25200940-25201090	HCM	heart:	n/a	n/a
37	CTCF	chr20:25200956-25201125	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr20:25201000-25201150	SK-N-SH_RA	brain:	n/a	n/a
39	SMC3	chr20:25200868-25201131	GM12878	blood:	n/a	n/a
40	CTCF	chr20:25200940-25201090	AG04450	lung:	n/a	n/a
41	CTCF	chr20:25200960-25201110	AG04449	skin:	n/a	n/a
42	CTCF	chr20:25201000-25201150	HMEC	breast:	n/a	n/a
43	TCF12	chr20:25200777-25201161	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr20:25200900-25201050	HA-sp	spinal cord:	n/a	n/a
45	ZBTB7A	chr20:25200897-25201150	HepG2	liver:	n/a	n/a
46	CEBPB	chr20:25200618-25201053	A549	lung:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200804-25200817
47	CTCF	chr20:25200960-25201110	HMEC	breast:	n/a	n/a
48	CEBPB	chr20:25200611-25201102	K562	blood:	n/a	chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200806-25200815 chr20:25200804-25200815 chr20:25200804-25200817
49	CTCF	chr20:25200900-25201050	NHEK	skin:	n/a	n/a
50	CTCF	chr20:25200982-25201082	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25200007..25207026-chr20:25227086..25230373,11	MCF-7	breast:
2	chr20:25199530..25201594-chr20:25205299..25208068,2	MCF-7	breast:
3	chr20:25188229..25190332-chr20:25200782..25202362,2	K562	blood:
4	chr20:25175979..25179968-chr20:25200206..25203711,4	MCF-7	breast:
5	chr20:25200658..25202199-chr20:25202354..25203959,2	MCF-7	breast:
6	chr20:25119622..25120296-chr20:25200777..25201493,2	MCF-7	breast:

Variant related genes	Relation type
ENTPD6	TF binding region
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction
ENSG00000268302	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]
rs58953621	1.00[EUR][1000 genomes]
rs59082275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];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	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6050451	0.81[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	0.88[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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
2	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
3	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:25186400-25203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:25189000-25203000	Weak transcription	K562	blood
8	chr20:25190200-25202800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:25190200-25202800	Strong transcription	Fetal Intestine Small	intestine
10	chr20:25190200-25206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr20:25190400-25201200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:25190400-25201600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr20:25190400-25201800	Strong transcription	Adipose Nuclei	Adipose
14	chr20:25190400-25202000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:25190400-25202200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:25190400-25202200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:25190400-25202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr20:25190400-25202200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr20:25190400-25202400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:25190400-25202400	Strong transcription	Primary T cells from cord blood	blood
21	chr20:25190400-25202400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr20:25190400-25202600	Strong transcription	Spleen	Spleen
23	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:25190400-25202800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:25190400-25202800	Strong transcription	Brain Cingulate Gyrus	brain
26	chr20:25190400-25202800	Strong transcription	Placenta	Placenta
27	chr20:25190400-25203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr20:25190400-25203000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:25190400-25203000	Strong transcription	Fetal Intestine Large	intestine
30	chr20:25190400-25203000	Strong transcription	NHLF	lung
31	chr20:25190400-25203200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr20:25190400-25203200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:25190400-25203400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr20:25190400-25203400	Strong transcription	Dnd41	blood
35	chr20:25190400-25203600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr20:25190400-25205200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr20:25190400-25207200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr20:25190400-25207200	Strong transcription	Fetal Stomach	stomach
39	chr20:25190400-25207200	Strong transcription	Ovary	ovary
40	chr20:25190600-25202000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:25190600-25202200	Strong transcription	Colon Smooth Muscle	Colon
42	chr20:25190600-25202400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr20:25190600-25207000	Strong transcription	Fetal Brain Female	brain
44	chr20:25190600-25207200	Strong transcription	Brain Germinal Matrix	brain
45	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
46	chr20:25191000-25203800	Weak transcription	HUVEC	blood vessel
47	chr20:25191600-25203200	Strong transcription	Brain Hippocampus Middle	brain
48	chr20:25191600-25204200	Strong transcription	Brain Angular Gyrus	brain
49	chr20:25192000-25201400	Strong transcription	Gastric	stomach
50	chr20:25192000-25202800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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