Variant report

Variant	rs534190199
Chromosome Location	chr19:40168896-40168897
allele	-/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	FOXA2	chr19:40168601-40169214	HepG2	liver:	n/a	n/a
2	STAT3	chr19:40168781-40169082	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
3	MTA3	chr19:40168891-40170844	GM12878	blood:	n/a	n/a
4	FOXA2	chr19:40168480-40169086	A549	lung:	n/a	n/a
5	MAFK	chr19:40168623-40168913	Hela-S3	cervix:	n/a	chr19:40168738-40168753
6	NFIC	chr19:40168553-40170977	GM12878	blood:	n/a	n/a
7	MAFK	chr19:40168580-40168938	HepG2	liver:	n/a	chr19:40168738-40168753
8	IKZF1	chr19:40168811-40169211	GM12878	blood:	n/a	n/a
9	MAFF	chr19:40168586-40168942	HepG2	liver:	n/a	chr19:40168736-40168754
10	FOXA1	chr19:40168522-40169018	HepG2	liver:	n/a	chr19:40168778-40168793
11	STAT3	chr19:40168678-40169057	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
12	MAX	chr19:40168547-40169052	MCF-7	breast:	n/a	n/a
13	MAFK	chr19:40168583-40168936	HepG2	liver:	n/a	chr19:40168738-40168753
14	STAT3	chr19:40168692-40169129	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
15	EBF1	chr19:40168815-40171812	GM12878	blood:	n/a	n/a
16	FOXA1	chr19:40168612-40168903	ECC-1	luminal epithelium:	n/a	chr19:40168778-40168793
17	FOXA1	chr19:40168608-40169026	HepG2	liver:	n/a	chr19:40168778-40168793
18	MYC	chr19:40168742-40169057	MCF10A-Er-Src	breast:	n/a	n/a
19	FOXA2	chr19:40168483-40169006	A549	lung:	n/a	n/a
20	MTA3	chr19:40168531-40172519	GM12878	blood:	n/a	n/a
21	FOS	chr19:40168741-40168941	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr19:40168788-40169120	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
23	PRDM1	chr19:40168623-40169061	Hela-S3	cervix:	n/a	chr19:40168899-40168913 chr19:40168837-40168851 chr19:40168838-40168851 chr19:40168900-40168913 chr19:40168836-40168851
24	MYC	chr19:40168715-40169061	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT1	chr19:40168657-40169174	Hela-S3	cervix:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168932-40168946 chr19:40168839-40168850
26	FOXA1	chr19:40168614-40168929	HepG2	liver:	n/a	chr19:40168778-40168793
27	FOXA1	chr19:40168597-40168998	T-47D	breast:	n/a	chr19:40168778-40168793
28	FOXA1	chr19:40168548-40168896	HepG2	liver:	n/a	chr19:40168778-40168793
29	FOXA1	chr19:40168559-40168933	T-47D	breast:	n/a	chr19:40168778-40168793

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40168876-40168926	IMR90	lung:	fetal
2	chr19:40168876-40168926	AG04450	lung:	fetal
3	chr19:40168876-40168926	A549	lung:	n/a
4	chr19:40168876-40168926	SK-N-SH_RA	brain:	n/a
5	chr19:40168876-40168926	HEK293	kidney:	embryo
6	chr19:40168876-40168926	NH-A	brain:	n/a
7	chr19:40168876-40168926	GM12878	blood:	n/a
8	chr19:40168876-40168926	HepG2	liver:	n/a
9	chr19:40168876-40168926	HCPEpiC	choroid plexus:	n/a
10	chr19:40168876-40168926	Hepatocyte	liver:	n/a
11	chr19:40168876-40168926	GM12892	blood:	n/a
12	chr19:40168876-40168926	PANC-1	pancreas:	n/a
13	chr19:40168876-40168926	ECC-1	luminal epithelium:	n/a
14	chr19:40168876-40168926	SKMC	muscle:	n/a
15	chr19:40168876-40168926	HRPEpiC	eye:	n/a
16	chr19:40168876-40168926	HEEpiC	esophagus:	n/a
17	chr19:40168876-40168926	HRCEpiC	kidney:	n/a
18	chr19:40168876-40168926	T-47D	breast:	n/a
19	chr19:40168876-40168926	NHBE	bronchial:	n/a
20	chr19:40168876-40168926	PrEC	prostate:	n/a
21	chr19:40168876-40168926	HCT-116	colon:	n/a
22	chr19:40168876-40168926	AoSMC	blood vessel:	n/a
23	chr19:40168876-40168926	ovcar-3	ovarian:	n/a
24	chr19:40168876-40168926	HL-60	blood:	n/a
25	chr19:40168876-40168926	HAEpiC	amniotic membrane:	n/a
26	chr19:40168876-40168926	MCF-7	breast:	n/a
27	chr19:40168876-40168926	MCF10A-Er-Src	breast:	n/a
28	chr19:40168876-40168926	HPAEpiC	pulmonary alveolar:	n/a
29	chr19:40168876-40168926	LNCaP	prostate:	n/a
30	chr19:40168876-40168926	K562	blood:	n/a
31	chr19:40168876-40168926	NT2-D1	testis:	n/a
32	chr19:40168876-40168926	HCF	heart:	n/a
33	chr19:40168876-40168926	PFSK-1	brain:	n/a
34	chr19:40168876-40168926	BE2_C	brain:	n/a
35	chr19:40168876-40168926	SK-N-SH	brain:	n/a
36	chr19:40168876-40168926	AG04449	skin:	fetal
37	chr19:40168876-40168926	NB4	blood:	n/a
38	chr19:40168876-40168926	U87	brain:	n/a
39	chr19:40168876-40168926	HCM	heart:	n/a
40	chr19:40168876-40168926	BJ	skin:	n/a
41	chr19:40168876-40168926	CMK	blood:	n/a
42	chr19:40168876-40168926	SK-N-MC	brain:	n/a
43	chr19:40168876-40168926	HRE	kidney:	n/a
44	chr19:40168876-40168926	GM12891	blood:	n/a
45	chr19:40168876-40168926	SAEC	small airway:	n/a
46	chr19:40168876-40168926	GM19239	blood:	n/a
47	chr19:40168876-40168926	GM06990	blood:	n/a
48	chr19:40168876-40168926	AG09319	gingival:	n/a
49	chr19:40168876-40168926	Caco-2	colon:	n/a
50	chr19:40168876-40168926	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40166260..40168931-chr19:40253973..40255544,2	MCF-7	breast:
2	chr19:40166471..40169299-chr19:40170755..40172585,2	K562	blood:
3	chr19:40168776..40170659-chr19:40171070..40173926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226025	TF binding region
ENSG00000226025	CpG island
ENSG00000226025	Chromatin interaction

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	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv2482	chr19:40125797-40170766	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3413868	chr19:40130700-40184720	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv960763	chr19:40168890-40177573	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40162600-40169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40166200-40169600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr19:40166200-40169600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr19:40167400-40169600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr19:40168000-40169800	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr19:40168200-40170000	Enhancers	Fetal Muscle Leg	muscle
7	chr19:40168200-40170400	Enhancers	Placenta	Placenta
8	chr19:40168400-40170200	Enhancers	Psoas Muscle	Psoas
9	chr19:40168400-40170600	Enhancers	Left Ventricle	heart
10	chr19:40168400-40170600	Enhancers	HepG2	liver
11	chr19:40168400-40171200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:40168600-40169200	Flanking Active TSS	Liver	Liver
13	chr19:40168600-40169200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:40168600-40169400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:40168600-40169600	Enhancers	Duodenum Mucosa	Duodenum
16	chr19:40168600-40169800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr19:40168600-40169800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr19:40168600-40169800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr19:40168600-40170000	Enhancers	Gastric	stomach
20	chr19:40168600-40170400	Enhancers	Brain Anterior Caudate	brain
21	chr19:40168600-40170600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:40168600-40170600	Enhancers	Adipose Nuclei	Adipose
23	chr19:40168600-40170600	Enhancers	Lung	lung
24	chr19:40168600-40170600	Enhancers	Pancreas	Pancrea
25	chr19:40168600-40170600	Enhancers	Right Ventricle	heart
26	chr19:40168600-40170800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr19:40168600-40171600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:40168600-40172600	Flanking Active TSS	GM12878-XiMat	blood
29	chr19:40168800-40169000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr19:40168800-40169000	Enhancers	Colonic Mucosa	Colon
31	chr19:40168800-40169000	Flanking Active TSS	A549	lung
32	chr19:40168800-40169200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr19:40168800-40169800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr19:40168800-40169800	Weak transcription	Esophagus	oesophagus
35	chr19:40168800-40170800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:40168800-40171200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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