Variant report

Variant	rs558725490
Chromosome Location	chr4:1231407-1231408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1230058-1232262	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:1230258-1232236	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:1231075-1231695	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:1230865-1231831	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr4:1230263-1231786	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:1230089-1232190	GM12892	blood:	n/a	n/a
7	POU2F2	chr4:1230888-1231834	GM12891	blood:	n/a	n/a
8	POLR2A	chr4:1230046-1232219	GM12892	blood:	n/a	n/a
9	POLR2A	chr4:1231099-1231798	GM12891	blood:	n/a	n/a
10	POU2F2	chr4:1231263-1231626	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:1230086-1232145	GM12878	blood:	n/a	n/a
12	FOSL2	chr4:1231280-1231636	HepG2	liver:	n/a	n/a
13	EP300	chr4:1231360-1231584	GM12878	blood:	n/a	n/a
14	HEY1	chr4:1231282-1231609	HepG2	liver:	n/a	n/a
15	ZBTB33	chr4:1231280-1231767	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:1231365-1231603	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:1231317-1231764	A549	lung:	n/a	n/a
18	POU2F2	chr4:1231225-1231717	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:1230161-1231979	GM12892	blood:	n/a	n/a
20	POLR2A	chr4:1230809-1232183	GM12891	blood:	n/a	n/a
21	POLR2A	chr4:1231279-1231585	A549	lung:	n/a	n/a
22	POU2F2	chr4:1231163-1231862	GM12891	blood:	n/a	n/a
23	POLR2A	chr4:1231033-1231641	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr4:1230117-1232164	GM12891	blood:	n/a	n/a
25	POLR2A	chr4:1230220-1232117	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:1230033-1232152	GM12892	blood:	n/a	n/a
27	POLR2A	chr4:1231138-1231499	K562	blood:	n/a	n/a
28	POLR2A	chr4:1230241-1231842	GM12878	blood:	n/a	n/a
29	PBX3	chr4:1231358-1231489	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr4:1231401-1231533	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:976786..978609-chr4:1230405..1232762,2	K562	blood:
2	chr4:1144843..1147526-chr4:1230222..1232389,2	MCF-7	breast:
3	chr4:1230672..1232310-chr4:1283727..1285762,2	K562	blood:

No data

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000227189	Chromatin interaction
ENSG00000215367	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
13	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
19	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
21	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
22	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
23	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
24	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
27	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
28	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
29	esv10056	chr4:1230368-1231788	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
30	esv1844406	chr4:1230397-1243775	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
31	esv3409612	chr4:1230802-1233300	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
32	esv1836927	chr4:1231363-1244037	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
4	chr4:1211400-1235400	Weak transcription	Small Intestine	intestine
5	chr4:1211600-1235400	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:1212600-1237000	Strong transcription	Dnd41	blood
7	chr4:1214200-1235600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:1214200-1236800	Strong transcription	Primary T cells from cord blood	blood
9	chr4:1214400-1235200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:1214400-1235600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr4:1214400-1236400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:1214400-1238400	Strong transcription	Thymus	Thymus
13	chr4:1214600-1235800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:1214600-1236200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:1215000-1235200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:1215000-1236000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:1215400-1236000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr4:1215800-1235600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:1216400-1235400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:1216400-1236000	Strong transcription	Fetal Thymus	thymus
21	chr4:1216600-1236000	Strong transcription	GM12878-XiMat	blood
22	chr4:1217200-1235400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:1217200-1235800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:1217600-1235200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:1218200-1234600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr4:1218800-1235400	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr4:1219000-1235400	Strong transcription	Gastric	stomach
28	chr4:1219000-1240200	Weak transcription	Hela-S3	cervix
29	chr4:1219800-1234800	Strong transcription	Fetal Intestine Large	intestine
30	chr4:1220600-1235400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:1221600-1236400	Weak transcription	Fetal Heart	heart
32	chr4:1221600-1240200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:1221800-1236400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:1222000-1240800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:1222600-1236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:1223000-1236600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:1223200-1236800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:1223600-1234200	Strong transcription	Osteobl	bone
39	chr4:1223600-1234800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:1223800-1236200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:1224000-1235400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:1225000-1240200	Weak transcription	K562	blood
43	chr4:1226800-1232200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:1226800-1235000	Strong transcription	Brain Substantia Nigra	brain
45	chr4:1227000-1235200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:1227200-1235200	Strong transcription	HepG2	liver
47	chr4:1227600-1234800	Strong transcription	Colonic Mucosa	Colon
48	chr4:1227600-1235800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr4:1227800-1236600	Strong transcription	Fetal Brain Female	brain
50	chr4:1228000-1232800	Weak transcription	Stomach Mucosa	stomach

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