Variant report

Variant	rs540589341
Chromosome Location	chr4:670474-670475
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	TCF12	chr4:670073-670494	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:667917-670486	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:667464-672151	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:670335-670810	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:670388-670847	U87	brain:	n/a	n/a
6	POLR2A	chr4:667656-672822	GM19099	blood:	n/a	n/a
7	POLR2A	chr4:670394-670847	U87	brain:	n/a	n/a
8	POLR2A	chr4:667899-673815	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:670030-671393	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:670412-673685	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:668697-671413	GM12891	blood:	n/a	n/a
12	ZNF143	chr4:669798-670706	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:667894-670508	GM12892	blood:	n/a	n/a
14	USF1	chr4:670450-670746	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:667908-672199	GM12878	blood:	n/a	n/a
16	CTCF	chr4:670354-670569	GM19239	blood:	n/a	n/a
17	POLR2A	chr4:670175-671004	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:670447-670837	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr4:667840-672164	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr4:670090-670563	GM12891	blood:	n/a	n/a
21	POLR2A	chr4:670376-671012	HepG2	liver:	n/a	n/a
22	CTCF	chr4:670420-670570	GM12873	blood:	n/a	n/a
23	POLR2A	chr4:669596-670848	HepG2	liver:	n/a	n/a
24	RELA	chr4:669600-670482	GM19193	blood:	n/a	n/a
25	USF2	chr4:669680-670761	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:669705-672344	ECC-1	luminal epithelium:	n/a	n/a
27	EBF1	chr4:669615-670857	GM12878	blood:	n/a	chr4:670830-670839 chr4:670724-670734
28	TCF3	chr4:670029-670949	GM12878	blood:	n/a	chr4:670900-670910 chr4:670842-670855 chr4:670795-670808 chr4:670838-670852 chr4:670793-670803
29	MTA3	chr4:667832-670995	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:670373-673590	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXM1	chr4:669787-670502	GM12878	blood:	n/a	n/a
32	POLR2A	chr4:667552-670868	GM12892	blood:	n/a	n/a
33	POLR2A	chr4:670102-670825	K562	blood:	n/a	n/a
34	POLR2A	chr4:670457-670607	Hela-S3	cervix:	n/a	n/a
35	PAX5	chr4:670023-670888	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:667550-672298	GM15510	blood:	n/a	n/a
37	HMGN3	chr4:670239-670562	K562	blood:	n/a	n/a
38	POLR2A	chr4:667573-670806	GM18526	blood:	n/a	n/a
39	CTCF	chr4:670051-670486	GM12878	blood:	n/a	chr4:670289-670302
40	POLR2A	chr4:666866-675998	K562	blood:	n/a	n/a
41	POLR2A	chr4:667409-672803	GM18505	blood:	n/a	n/a
42	POLR2A	chr4:667311-672325	GM19193	blood:	n/a	n/a
43	POLR2A	chr4:670078-670810	GM12878	blood:	n/a	n/a
44	ELF1	chr4:670473-671133	GM12878	blood:	n/a	n/a
45	POLR2A	chr4:667296-675255	MCF10A-Er-Src	breast:	n/a	n/a
46	RUNX3	chr4:669705-670539	GM12878	blood:	n/a	n/a
47	BRCA1	chr4:669929-670601	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:669990-673196	K562	blood:	n/a	n/a
49	POLR2A	chr4:667912-670842	GM12878	blood:	n/a	n/a
50	NFATC1	chr4:669917-670899	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:666295..671517-chr4:698228..703248,8	MCF-7	breast:
2	chr4:669988..672792-chr4:681146..683044,2	K562	blood:
3	chr4:666292..671732-chr4:694079..701503,8	MCF-7	breast:
4	chr4:493062..494777-chr4:668037..670861,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-2	chr4:668129-671710	NONHSAT094599

Variant related genes	Relation type
MYL5	TF binding region
ATP5I	TF binding region
ENSG00000185619	Chromatin interaction
ENSG00000169026	Chromatin interaction
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	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
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	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
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv10413	chr4:667204-684301	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv593208	chr4:668000-682233	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv878250	chr4:668567-683842	Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv878251	chr4:669857-683842	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv878252	chr4:669857-685993	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:668600-670800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr4:668800-670600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:668800-670800	Flanking Active TSS	GM12878-XiMat	blood
4	chr4:668800-671200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr4:668800-674400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:669000-672200	Enhancers	Spleen	Spleen
7	chr4:669200-670600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:669200-670800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:669200-671000	Enhancers	Fetal Heart	heart
10	chr4:669200-671000	Enhancers	Fetal Thymus	thymus
11	chr4:669200-671200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr4:669200-671400	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:669200-672000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:669200-672600	Enhancers	Esophagus	oesophagus
15	chr4:669200-672600	Enhancers	Fetal Intestine Large	intestine
16	chr4:669200-673000	Enhancers	Pancreas	Pancrea
17	chr4:669200-674200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:669200-674400	Weak transcription	Fetal Lung	lung
19	chr4:669400-670600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:669400-670600	Genic enhancers	Fetal Intestine Small	intestine
21	chr4:669400-670600	Enhancers	K562	blood
22	chr4:669400-671000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr4:669400-671200	Enhancers	Primary B cells from cord blood	blood
24	chr4:669400-671400	Enhancers	Psoas Muscle	Psoas
25	chr4:669400-672200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:669400-672800	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:669400-674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:669400-674200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:669400-674200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:669400-674200	Weak transcription	NH-A	brain
31	chr4:669400-674400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:669400-674400	Weak transcription	Ovary	ovary
33	chr4:669400-674400	Weak transcription	Right Atrium	heart
34	chr4:669400-674600	Enhancers	Placenta	Placenta
35	chr4:669400-674600	Weak transcription	HUVEC	blood vessel
36	chr4:669600-670600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:669600-670800	Weak transcription	Colonic Mucosa	Colon
38	chr4:669600-671000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:669600-671000	Weak transcription	HMEC	breast
40	chr4:669600-671400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:669600-671400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:669600-671600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:669600-671800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:669600-673800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:669600-674000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:669600-674000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:669600-674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:669600-674000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:669600-674000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr4:669600-674200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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