Variant report

Variant	rs557353420
Chromosome Location	chr4:1209528-1209529
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	BCL11A	chr4:1209157-1209563	GM12878	blood:	n/a	n/a
2	SPI1	chr4:1209283-1209547	GM12878	blood:	n/a	n/a
3	EP300	chr4:1208922-1209837	GM12878	blood:	n/a	chr4:1209068-1209084
4	PAX5	chr4:1209020-1209543	GM12878	blood:	n/a	n/a
5	ZEB1	chr4:1209107-1209882	GM12878	blood:	n/a	chr4:1209683-1209694
6	TCF3	chr4:1208859-1210344	GM12878	blood:	n/a	n/a
7	MAX	chr4:1209167-1209719	GM12878	blood:	n/a	n/a
8	FOXM1	chr4:1208988-1209803	GM12878	blood:	n/a	n/a
9	FOXM1	chr4:1209129-1209725	GM12878	blood:	n/a	n/a
10	CEBPB	chr4:1209279-1209582	GM12878	blood:	n/a	n/a
11	SMC3	chr4:1209213-1209528	GM12878	blood:	n/a	n/a
12	EP300	chr4:1209235-1209676	GM12878	blood:	n/a	n/a
13	SP1	chr4:1209279-1209632	GM12878	blood:	n/a	n/a
14	YY1	chr4:1209198-1209592	GM12892	blood:	n/a	n/a
15	EGR1	chr4:1208932-1209567	GM12878	blood:	n/a	chr4:1209071-1209086 chr4:1209249-1209260 chr4:1209247-1209262 chr4:1209072-1209085 chr4:1209245-1209259
16	POLR2A	chr4:1208794-1209565	GM12878	blood:	n/a	n/a
17	POU2F2	chr4:1208972-1209651	GM12891	blood:	n/a	n/a
18	POLR2A	chr4:1208842-1209698	GM12891	blood:	n/a	n/a
19	BCLAF1	chr4:1208969-1209695	GM12878	blood:	n/a	chr4:1209624-1209633
20	NFATC1	chr4:1208915-1209677	GM12878	blood:	n/a	n/a
21	RUNX3	chr4:1208852-1210386	GM12878	blood:	n/a	n/a
22	TCF12	chr4:1209060-1209872	GM12878	blood:	n/a	n/a
23	ELF1	chr4:1209196-1209615	GM12878	blood:	n/a	n/a
24	YY1	chr4:1209088-1209560	GM12878	blood:	n/a	n/a
25	TAF1	chr4:1209227-1209569	GM12878	blood:	n/a	n/a
26	POU2F2	chr4:1208877-1209641	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:1208736-1211035	GM12892	blood:	n/a	n/a
28	MTA3	chr4:1208835-1211238	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:1208925-1209797	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:1208947-1209642	GM12892	blood:	n/a	n/a
31	NFIC	chr4:1209152-1209701	GM12878	blood:	n/a	n/a
32	POLR2A	chr4:1208946-1209930	GM18505	blood:	n/a	n/a
33	PAX5	chr4:1209225-1209531	GM12878	blood:	n/a	n/a
34	CEBPB	chr4:1209147-1209683	GM12878	blood:	n/a	n/a
35	TBL1XR1	chr4:1209285-1209627	GM12878	blood:	n/a	n/a
36	TCF12	chr4:1209109-1209870	GM12878	blood:	n/a	n/a
37	ZEB1	chr4:1209347-1209749	GM12878	blood:	n/a	chr4:1209683-1209694
38	ELF1	chr4:1208687-1211263	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:1209517-1209536	HepG2	liver:	n/a	n/a
40	BHLHE40	chr4:1209295-1209629	GM12878	blood:	n/a	n/a
41	CHD2	chr4:1209215-1209552	GM12878	blood:	n/a	n/a
42	SPI1	chr4:1209282-1209603	GM12891	blood:	n/a	n/a
43	EGR1	chr4:1209311-1209535	GM12878	blood:	n/a	n/a
44	POLR2A	chr4:1208954-1209638	SK-N-MC	brain:	n/a	n/a
45	EP300	chr4:1209198-1209622	GM12878	blood:	n/a	n/a
46	PAX5	chr4:1209212-1209574	GM12878	blood:	n/a	n/a
47	RUNX3	chr4:1208870-1209923	GM12878	blood:	n/a	n/a
48	ATF2	chr4:1208963-1209677	GM12878	blood:	n/a	n/a
49	TCF3	chr4:1208965-1209830	GM12878	blood:	n/a	n/a
50	PML	chr4:1209156-1209622	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1209494..1211546-chr4:1218177..1220594,3	MCF-7	breast:
2	chr2:86422601..86423306-chr4:1209197..1209717,2	MCF-7	breast:
3	chr4:1203383..1207466-chr4:1208474..1210757,3	K562	blood:
4	chr4:1207031..1209938-chr4:1240960..1243998,4	K562	blood:
5	chr2:86422281..86424225-chr4:1209194..1210696,2	K562	blood:

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000196810	Chromatin interaction
ENSG00000273080	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	nsv966246	chr4:1205017-1210824	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
25	esv3436317	chr4:1208602-1211100	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	esv3355881	chr4:1209202-1211700	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 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	chr4:1195200-1214600	Weak transcription	A549	lung
2	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
3	chr4:1198000-1211200	Genic enhancers	Fetal Stomach	stomach
4	chr4:1201600-1211600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:1201800-1210000	Strong transcription	Thymus	Thymus
6	chr4:1202400-1210000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:1202600-1210200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:1202800-1210200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:1202800-1218000	Weak transcription	Fetal Brain Male	brain
10	chr4:1203000-1209600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:1203000-1210200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:1203200-1217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:1203400-1210200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:1203400-1213000	Weak transcription	Fetal Kidney	kidney
15	chr4:1203800-1223000	Strong transcription	Osteobl	bone
16	chr4:1204000-1211600	Genic enhancers	Esophagus	oesophagus
17	chr4:1204000-1218000	Weak transcription	K562	blood
18	chr4:1204200-1212600	Genic enhancers	Fetal Muscle Leg	muscle
19	chr4:1204400-1210000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:1204400-1210400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:1204400-1210800	Strong transcription	Fetal Intestine Large	intestine
22	chr4:1204400-1211600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:1204400-1211600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:1204400-1211600	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr4:1204400-1212000	Strong transcription	NHEK	skin
26	chr4:1204400-1227200	Strong transcription	Fetal Intestine Small	intestine
27	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:1204600-1210000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:1204600-1210200	Weak transcription	Fetal Heart	heart
30	chr4:1204600-1220400	Strong transcription	Liver	Liver
31	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:1204800-1211000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:1204800-1212000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr4:1204800-1213800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:1204800-1226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
37	chr4:1205000-1210000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:1205000-1210200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:1205000-1210600	Weak transcription	Small Intestine	intestine
40	chr4:1205000-1211000	Weak transcription	Right Atrium	heart
41	chr4:1205000-1213400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:1205000-1226200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:1205200-1210000	Strong transcription	Right Ventricle	heart
44	chr4:1205200-1210400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:1205200-1211800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:1205200-1218000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:1205400-1226800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:1205600-1210000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:1205800-1210400	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr4:1205800-1211400	Strong transcription	Placenta Amnion	Placenta Amnion

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