Variant report

Variant	rs540522906
Chromosome Location	chr19:18543717-18543718
allele	C/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	YY1	chr19:18543495-18544431	GM12878	blood:	n/a	chr19:18544283-18544294 chr19:18544285-18544294
2	POLR2A	chr19:18543524-18545258	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:18543104-18544416	GM12878	blood:	n/a	n/a
4	BCL3	chr19:18543616-18544387	K562	blood:	n/a	chr19:18543740-18543749 chr19:18543741-18543750 chr19:18544283-18544292 chr19:18544281-18544294 chr19:18544100-18544113
5	MAX	chr19:18543515-18545245	K562	blood:	n/a	chr19:18544474-18544484 chr19:18545007-18545017
6	POLR2A	chr19:18543590-18544386	GM12891	blood:	n/a	n/a
7	POU2F2	chr19:18543546-18544287	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:18538551-18551124	K562	blood:	n/a	n/a
9	BCLAF1	chr19:18543587-18544362	GM12878	blood:	n/a	chr19:18543740-18543749 chr19:18543741-18543750 chr19:18544283-18544292 chr19:18544281-18544294 chr19:18544100-18544113
10	ELF1	chr19:18543656-18544411	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:18543470-18548238	PANC-1	pancreas:	n/a	n/a
12	TCF3	chr19:18543672-18544433	GM12878	blood:	n/a	n/a
13	HEY1	chr19:18543533-18544433	K562	blood:	n/a	chr19:18544291-18544306 chr19:18544272-18544287 chr19:18544281-18544296 chr19:18544138-18544153
14	CHD2	chr19:18543582-18545221	K562	blood:	n/a	chr19:18544477-18544487 chr19:18544220-18544230 chr19:18544038-18544048 chr19:18544482-18544492
15	POLR2A	chr19:18534926-18553479	K562	blood:	n/a	n/a
16	YY1	chr19:18543668-18544465	GM12878	blood:	n/a	chr19:18544283-18544294 chr19:18544285-18544294
17	BCL3	chr19:18543538-18544439	GM12878	blood:	n/a	chr19:18543740-18543749 chr19:18543741-18543750 chr19:18544283-18544292 chr19:18544281-18544294 chr19:18544100-18544113
18	STAT5A	chr19:18543706-18543916	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:18543447-18547067	K562	blood:	n/a	n/a
20	POLR2A	chr19:18543681-18544314	HepG2	liver:	n/a	n/a
21	STAT5A	chr19:18542897-18544436	GM12878	blood:	n/a	n/a
22	ATF2	chr19:18543709-18544259	GM12878	blood:	n/a	n/a
23	YY1	chr19:18543509-18544429	GM12892	blood:	n/a	chr19:18544283-18544294 chr19:18544285-18544294
24	POLR2A	chr19:18543626-18552057	K562	blood:	n/a	n/a
25	EGR1	chr19:18543427-18545145	K562	blood:	n/a	chr19:18544024-18544035 chr19:18544742-18544755 chr19:18544471-18544484 chr19:18544470-18544485 chr19:18544300-18544310 chr19:18544742-18544752 chr19:18544044-18544053 chr19:18544043-18544056 chr19:18544025-18544035 chr19:18544741-18544756 chr19:18544040-18544054 chr19:18544471-18544484 chr19:18544283-18544296 chr19:18544476-18544486 chr19:18544742-18544755 chr19:18544833-18544843 chr19:18544833-18544846 chr19:18544044-18544054 chr19:18544473-18544483
26	POLR2A	chr19:18543410-18544460	K562	blood:	n/a	n/a
27	ZNF263	chr19:18543530-18544238	HEK293-T-REx	kidney:	n/a	n/a
28	YY1	chr19:18543684-18544417	H1-hESC	embryonic stem cell:	n/a	chr19:18544283-18544294 chr19:18544285-18544294
29	POLR2A	chr19:18543527-18543737	MCF-7	breast:	n/a	n/a
30	ELF1	chr19:18543423-18544469	GM12878	blood:	n/a	n/a
31	CEBPB	chr19:18543562-18544197	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:18543518-18544434	U87	brain:	n/a	n/a
33	POU2F2	chr19:18543575-18544237	GM12891	blood:	n/a	n/a
34	BCLAF1	chr19:18543571-18544241	GM12878	blood:	n/a	chr19:18543740-18543749 chr19:18543741-18543750 chr19:18544100-18544113
35	MTA3	chr19:18543414-18544507	GM12878	blood:	n/a	n/a
36	MYC	chr19:18543688-18543726	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr19:18543627-18544346	GM12892	blood:	n/a	n/a
38	POLR2A	chr19:18543463-18546622	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:18543697-18544610	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr19:18543438-18544542	GM12891	blood:	n/a	n/a
41	POLR2A	chr19:18542837-18543833	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr19:18543476-18544597	GM12892	blood:	n/a	n/a
43	POLR2A	chr19:18543673-18544485	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:18543467-18545389	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr19:18543469-18544190	MCF-7	breast:	n/a	n/a
46	POLR2A	chr19:18543712-18544456	HUVEC	blood vessel:	n/a	n/a
47	MAZ	chr19:18543589-18544626	GM12878	blood:	n/a	chr19:18544474-18544484
48	POLR2A	chr19:18543619-18544638	GM19193	blood:	n/a	n/a
49	POLR2A	chr19:18543512-18544440	GM12878	blood:	n/a	n/a
50	TEAD4	chr19:18543717-18544289	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12067124..12068647-chr19:18543710..18545740,2	K562	blood:
2	chr19:18527431..18533703-chr19:18536573..18544512,11	MCF-7	breast:
3	chr19:18384108..18395354-chr19:18534355..18544725,18	K562	blood:
4	chr19:18495466..18501669-chr19:18543275..18549976,8	K562	blood:
5	chr18:12067124..12068644-chr19:18543710..18545856,2	K562	blood:
6	chr19:18385251..18388025-chr19:18541664..18544540,2	K562	blood:
7	chr19:18484864..18486946-chr19:18543605..18545790,2	K562	blood:
8	chr19:18507454..18509649-chr19:18542288..18544063,2	K562	blood:

Variant related genes	Relation type
SSBP4	TF binding region
ENSG00000267533	Chromatin interaction
ENSG00000175489	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130518	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000267959	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking 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	162 gene(s)	inside rSNPs	diseases
3	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
7	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
8	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv911277	chr19:18520231-18552139	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
11	nsv911278	chr19:18526536-18550276	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
12	nsv911279	chr19:18533642-18550276	Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
13	nsv911280	chr19:18533642-18552139	Genic enhancers Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
15	esv3429815	chr19:18543377-18545925	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 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	chr19:18532800-18547600	Weak transcription	HepG2	liver
2	chr19:18537400-18543800	Weak transcription	NHEK	skin
3	chr19:18537400-18544000	Weak transcription	HMEC	breast
4	chr19:18538000-18547600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:18538000-18548400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:18539200-18544000	Enhancers	Fetal Heart	heart
7	chr19:18540600-18543800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:18540600-18543800	Genic enhancers	Fetal Muscle Leg	muscle
9	chr19:18540600-18543800	Genic enhancers	Fetal Stomach	stomach
10	chr19:18540800-18543800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:18540800-18543800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:18540800-18543800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:18540800-18543800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:18540800-18543800	Weak transcription	Osteobl	bone
15	chr19:18540800-18544000	Weak transcription	Gastric	stomach
16	chr19:18540800-18544000	Weak transcription	Small Intestine	intestine
17	chr19:18540800-18545400	Weak transcription	A549	lung
18	chr19:18541000-18543800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:18541000-18543800	Weak transcription	Brain Substantia Nigra	brain
20	chr19:18541000-18543800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:18541000-18543800	Weak transcription	HSMM	muscle
22	chr19:18541000-18543800	Weak transcription	NHDF-Ad	bronchial
23	chr19:18541000-18547800	Weak transcription	HSMMtube	muscle
24	chr19:18541200-18544200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:18541400-18543800	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr19:18541600-18543800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:18541600-18544000	Strong transcription	Dnd41	blood
28	chr19:18541600-18546800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:18541600-18548000	Weak transcription	Stomach Mucosa	stomach
30	chr19:18541800-18543800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:18541800-18545200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:18542400-18543800	Enhancers	Primary hematopoietic stem cells	blood
33	chr19:18542600-18543800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:18542600-18543800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr19:18542600-18543800	Genic enhancers	Fetal Thymus	thymus
36	chr19:18542600-18543800	Enhancers	Stomach Smooth Muscle	stomach
37	chr19:18542600-18548000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:18542800-18543800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:18542800-18544400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:18542800-18545800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:18543000-18543800	Genic enhancers	NHLF	lung
42	chr19:18543000-18544000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:18543000-18544000	Flanking Active TSS	GM12878-XiMat	blood
44	chr19:18543000-18544200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr19:18543200-18543800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr19:18543200-18543800	Enhancers	Placenta	Placenta
47	chr19:18543200-18544200	Flanking Active TSS	K562	blood
48	chr19:18543200-18544400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:18543200-18545400	Enhancers	Spleen	Spleen
50	chr19:18543400-18543800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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