Variant report

Variant	rs558924820
Chromosome Location	chr5:49962826-49962827
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	POLR2A	chr5:49961594-49964348	GM18526	blood:	n/a	n/a
2	TCF3	chr5:49962214-49964093	GM12878	blood:	n/a	chr5:49963139-49963153
3	POLR2A	chr5:49962175-49964285	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:49962582-49963078	PANC-1	pancreas:	n/a	n/a
5	GTF2F1	chr5:49962763-49962953	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr5:49962529-49964321	GM12892	blood:	n/a	n/a
7	POLR2A	chr5:49962403-49962998	HCT-116	colon:	n/a	n/a
8	PAX5	chr5:49962448-49963044	GM12878	blood:	n/a	n/a
9	EP300	chr5:49962458-49962870	H1-hESC	embryonic stem cell:	n/a	chr5:49962538-49962547
10	POLR2A	chr5:49962189-49964764	GM12892	blood:	n/a	n/a
11	POLR2A	chr5:49961505-49964690	GM12891	blood:	n/a	n/a
12	TCF7L2	chr5:49962272-49964233	HCT-116	colon:	n/a	n/a
13	POLR2A	chr5:49962201-49964373	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:49962143-49963976	HL-60	blood:	n/a	n/a
15	TAF1	chr5:49962714-49963022	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr5:49961945-49964411	IMR90	lung:	n/a	chr5:49963252-49963261 chr5:49963676-49963685
17	EP300	chr5:49962683-49964461	GM12878	blood:	n/a	chr5:49963354-49963370
18	STAT3	chr5:49962721-49962843	MCF10A-Er-Src	breast:	n/a	n/a
19	TEAD4	chr5:49962448-49962906	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:49962177-49964902	GM12892	blood:	n/a	n/a
21	POU2F2	chr5:49962614-49963105	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:49962114-49964801	H1-hESC	embryonic stem cell:	n/a	n/a
23	BCL11A	chr5:49962597-49963034	GM12878	blood:	n/a	n/a
24	PML	chr5:49962668-49964363	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:49962284-49962831	ProgFib	skin:	n/a	n/a
26	POLR2A	chr5:49961626-49964340	GM15510	blood:	n/a	n/a
27	TCF12	chr5:49962300-49964205	GM12878	blood:	n/a	n/a
28	BHLHE40	chr5:49962310-49962966	GM12878	blood:	n/a	chr5:49962437-49962453 chr5:49962350-49962366 chr5:49962434-49962450 chr5:49962398-49962414 chr5:49962351-49962367 chr5:49962358-49962374
29	ZBTB33	chr5:49962779-49963721	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:49962532-49964210	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr5:49961280-49964895	GM12892	blood:	n/a	n/a
32	POLR2A	chr5:49962166-49964359	GM12878	blood:	n/a	n/a
33	ELF1	chr5:49962138-49963932	GM12878	blood:	n/a	chr5:49963440-49963452 chr5:49963351-49963363
34	TAF1	chr5:49962572-49963036	GM12891	blood:	n/a	n/a
35	SP1	chr5:49962677-49964479	GM12878	blood:	n/a	chr5:49963094-49963104 chr5:49963174-49963183 chr5:49963094-49963103 chr5:49963090-49963104 chr5:49963173-49963185 chr5:49963202-49963211 chr5:49963196-49963210 chr5:49962734-49962745 chr5:49963201-49963215 chr5:49963173-49963185
36	POLR2A	chr5:49962439-49962876	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr5:49962630-49962916	MCF-7	breast:	n/a	n/a
38	POLR2A	chr5:49962184-49964822	GM12892	blood:	n/a	n/a
39	POU2F2	chr5:49962288-49964584	GM12878	blood:	n/a	chr5:49962360-49962372
40	FOXM1	chr5:49962630-49964451	GM12878	blood:	n/a	n/a
41	HEY1	chr5:49962585-49963123	HepG2	liver:	n/a	n/a
42	YY1	chr5:49962441-49962911	H1-hESC	embryonic stem cell:	n/a	chr5:49962542-49962551 chr5:49962537-49962551 chr5:49962536-49962550
43	RELA	chr5:49962276-49964270	GM12891	blood:	n/a	chr5:49963663-49963672 chr5:49963663-49963672
44	POLR2A	chr5:49962388-49964845	GM12891	blood:	n/a	n/a
45	SIN3AK20	chr5:49962171-49962842	PANC-1	pancreas:	n/a	n/a
46	IKZF1	chr5:49962641-49963009	GM12878	blood:	n/a	n/a
47	TCF12	chr5:49962565-49962846	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF1	chr5:49962639-49964474	GM12878	blood:	n/a	n/a
49	BCLAF1	chr5:49962387-49962943	GM12878	blood:	n/a	chr5:49962434-49962447 chr5:49962538-49962551 chr5:49962542-49962555 chr5:49962441-49962454
50	TCF12	chr5:49962564-49963356	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000271752	TF binding region
PARP8	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription 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	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv968172	chr5:49961360-49966431	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv968910	chr5:49961360-49980983	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49961600-49963000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:49961600-49963000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:49961600-49963200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr5:49961600-49964400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:49961600-49964600	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr5:49961600-49964800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:49961600-49964800	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:49961600-49965200	Active TSS	GM12878-XiMat	blood
9	chr5:49961600-49965400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:49961800-49963000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:49961800-49964400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:49961800-49964400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:49961800-49964400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:49961800-49964400	Active TSS	Colon Smooth Muscle	Colon
15	chr5:49961800-49964400	Active TSS	Esophagus	oesophagus
16	chr5:49961800-49964400	Active TSS	Fetal Stomach	stomach
17	chr5:49961800-49964400	Active TSS	Rectal Smooth Muscle	rectum
18	chr5:49961800-49964400	Active TSS	Right Atrium	heart
19	chr5:49961800-49964400	Active TSS	Small Intestine	intestine
20	chr5:49961800-49964400	Active TSS	Hela-S3	cervix
21	chr5:49961800-49964400	Active TSS	HSMMtube	muscle
22	chr5:49961800-49964400	Active TSS	NH-A	brain
23	chr5:49961800-49964600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:49961800-49964600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr5:49961800-49964600	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr5:49961800-49964600	Active TSS	Liver	Liver
27	chr5:49961800-49964600	Active TSS	Brain Germinal Matrix	brain
28	chr5:49961800-49964600	Active TSS	Fetal Brain Female	brain
29	chr5:49961800-49964600	Active TSS	Fetal Kidney	kidney
30	chr5:49961800-49964600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr5:49961800-49964800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:49961800-49964800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:49961800-49964800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:49961800-49964800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr5:49961800-49964800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:49961800-49964800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:49961800-49964800	Active TSS	Brain Angular Gyrus	brain
38	chr5:49961800-49964800	Active TSS	Brain Cingulate Gyrus	brain
39	chr5:49961800-49964800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:49961800-49964800	Active TSS	NHDF-Ad	bronchial
41	chr5:49961800-49964800	Active TSS	NHLF	lung
42	chr5:49961800-49965000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr5:49961800-49965000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr5:49961800-49965400	Active TSS	Thymus	Thymus
45	chr5:49961800-49965400	Active TSS	HMEC	breast
46	chr5:49962000-49963000	Active TSS	Adipose Nuclei	Adipose
47	chr5:49962000-49963000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr5:49962000-49963200	Active TSS	Fetal Muscle Trunk	muscle
49	chr5:49962000-49964000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:49962000-49964000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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