Variant report

Variant	rs550078240
Chromosome Location	chr19:40696909-40696910
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	chr19:40696641-40697721	A549	lung:	n/a	n/a
2	TBP	chr19:40696893-40696921	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF2	chr19:40696306-40696953	GM12878	blood:	n/a	n/a
4	FOXM1	chr19:40696296-40697034	GM12878	blood:	n/a	n/a
5	BCLAF1	chr19:40696348-40696956	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:40696410-40697357	U87	brain:	n/a	n/a
7	POLR2A	chr19:40696674-40697122	HepG2	liver:	n/a	n/a
8	FOXA2	chr19:40696648-40697608	A549	lung:	n/a	n/a
9	TBL1XR1	chr19:40696474-40697049	GM12878	blood:	n/a	n/a
10	E2F4	chr19:40696428-40697047	MCF10A-Er-Src	breast:	n/a	n/a
11	SIX5	chr19:40696795-40697450	K562	blood:	n/a	chr19:40697292-40697301 chr19:40696919-40696928 chr19:40697200-40697216 chr19:40697294-40697303 chr19:40696921-40696930
12	POLR2A	chr19:40696261-40697107	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:40696734-40697537	HEK293	kidney:	n/a	n/a
14	ELF1	chr19:40696759-40697422	K562	blood:	n/a	chr19:40697316-40697325 chr19:40697313-40697322 chr19:40697158-40697170
15	MAX	chr19:40696214-40698398	A549	lung:	n/a	n/a
16	POLR2A	chr19:40696657-40698101	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:40696898-40697113	HepG2	liver:	n/a	n/a
18	HEY1	chr19:40696559-40697473	HepG2	liver:	n/a	chr19:40697309-40697324 chr19:40696716-40696725
19	EBF1	chr19:40696571-40697003	GM12878	blood:	n/a	chr19:40696770-40696779 chr19:40696768-40696779 chr19:40696770-40696779 chr19:40696768-40696781
20	YY1	chr19:40696412-40697431	A549	lung:	n/a	chr19:40697314-40697325 chr19:40697316-40697325 chr19:40697319-40697333 chr19:40697313-40697322 chr19:40697319-40697328 chr19:40697233-40697242 chr19:40697313-40697327
21	POLR2A	chr19:40696518-40697424	SK-N-SH	brain:	n/a	n/a
22	RCOR1	chr19:40696367-40697254	K562	blood:	n/a	n/a
23	MAX	chr19:40696752-40697003	K562	blood:	n/a	n/a
24	CHD2	chr19:40696852-40697014	HepG2	liver:	n/a	n/a
25	RCOR1	chr19:40696711-40697041	HepG2	liver:	n/a	n/a
26	POLR2A	chr19:40696703-40697464	HUVEC	blood vessel:	n/a	n/a
27	MAX	chr19:40696423-40697440	Hela-S3	cervix:	n/a	n/a
28	MYC	chr19:40696394-40697423	K562	blood:	n/a	n/a
29	SIN3A	chr19:40696667-40698071	H1-hESC	embryonic stem cell:	n/a	chr19:40696898-40696907 chr19:40696890-40696901 chr19:40697557-40697570
30	REST	chr19:40696167-40699848	PANC-1	pancreas:	n/a	chr19:40697230-40697243 chr19:40696949-40696962 chr19:40697557-40697570 chr19:40697230-40697243 chr19:40697557-40697575 chr19:40697919-40697929
31	PML	chr19:40696229-40697458	GM12878	blood:	n/a	chr19:40696726-40696734
32	SIN3AK20	chr19:40695285-40697463	PANC-1	pancreas:	n/a	n/a
33	MAX	chr19:40696432-40697160	NB4	blood:	n/a	n/a
34	JUN	chr19:40695794-40697935	K562	blood:	n/a	chr19:40697375-40697384
35	MYC	chr19:40696474-40697460	NB4	blood:	n/a	n/a
36	POLR2A	chr19:40696711-40697466	A549	lung:	n/a	n/a
37	EP300	chr19:40696489-40696943	GM12878	blood:	n/a	chr19:40696857-40696873 chr19:40696888-40696904
38	YY1	chr19:40696357-40696957	GM12892	blood:	n/a	n/a
39	EP300	chr19:40696445-40697106	GM12878	blood:	n/a	chr19:40696857-40696873 chr19:40696888-40696904
40	USF1	chr19:40696398-40696975	A549	lung:	n/a	chr19:40696884-40696900
41	ETS1	chr19:40696383-40697437	A549	lung:	n/a	chr19:40696917-40696930 chr19:40697295-40697302 chr19:40697080-40697093 chr19:40696782-40696796 chr19:40697291-40697304 chr19:40697314-40697325 chr19:40697084-40697095 chr19:40697290-40697303 chr19:40696918-40696931
42	POLR2A	chr19:40696664-40698103	H1-neurons	neurons:	n/a	n/a
43	MXI1	chr19:40696487-40697205	K562	blood:	n/a	n/a
44	CEBPB	chr19:40696420-40696984	Hela-S3	cervix:	n/a	n/a
45	YY1	chr19:40696417-40697435	GM12878	blood:	n/a	chr19:40697314-40697325 chr19:40697316-40697325 chr19:40697319-40697333 chr19:40697313-40697322 chr19:40697319-40697328 chr19:40697233-40697242 chr19:40697313-40697327
46	GABPA	chr19:40696749-40697437	K562	blood:	n/a	n/a
47	BCL3	chr19:40696378-40697420	A549	lung:	n/a	chr19:40697314-40697323 chr19:40697229-40697242 chr19:40697343-40697356 chr19:40697309-40697322 chr19:40697313-40697326 chr19:40697317-40697326 chr19:40697379-40697392 chr19:40697312-40697325
48	JUND	chr19:40696336-40697569	A549	lung:	n/a	chr19:40696571-40696582 chr19:40697375-40697384
49	CREB1	chr19:40696650-40698092	A549	lung:	n/a	n/a
50	SIN3A	chr19:40696494-40697390	GM12878	blood:	n/a	chr19:40696898-40696907 chr19:40696890-40696901

No.	Distal block	Cell Line	Cell type
1	chr13:111367593..111368509-chr19:40696817..40697667,2	HCT-116	colon:
2	chr19:40695407..40698481-chr19:40788292..40792778,5	K562	blood:
3	chr19:40688006..40692388-chr19:40694622..40697525,4	K562	blood:
4	chr19:40476601..40478274-chr19:40696597..40698505,2	MCF-7	breast:
5	chr19:40695427..40698103-chr19:41080992..41083965,2	K562	blood:
6	chr19:40696418..40698830-chr19:40709554..40711978,2	K562	blood:
7	chr19:40688598..40690270-chr19:40694622..40697425,2	K562	blood:
8	chr19:40696492..40699360-chr19:41104510..41106083,2	MCF-7	breast:

Variant related genes	Relation type
MAP3K10	TF binding region
ENSG00000207631	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000221051	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv3426637	chr19:40696137-40698985	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv3389051	chr19:40696662-40698860	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv3427944	chr19:40696737-40699285	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40695800-40698000	Active TSS	GM12878-XiMat	blood
2	chr19:40695800-40698600	Active TSS	Osteobl	bone
3	chr19:40696000-40698400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:40696000-40698400	Active TSS	Brain Angular Gyrus	brain
5	chr19:40696200-40697000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr19:40696200-40697800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:40696200-40698000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:40696200-40698000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:40696200-40698000	Active TSS	Brain Anterior Caudate	brain
10	chr19:40696200-40698000	Active TSS	Brain Hippocampus Middle	brain
11	chr19:40696200-40698000	Active TSS	Psoas Muscle	Psoas
12	chr19:40696200-40698000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:40696200-40698200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:40696400-40697000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:40696400-40697000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:40696400-40697000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr19:40696400-40697000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:40696400-40697000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:40696400-40697000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:40696400-40697000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:40696400-40697000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr19:40696400-40697000	Flanking Active TSS	Dnd41	blood
23	chr19:40696400-40697000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:40696400-40697200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:40696400-40697200	Active TSS	Fetal Heart	heart
26	chr19:40696400-40697200	Flanking Active TSS	Placenta	Placenta
27	chr19:40696400-40697400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
28	chr19:40696400-40697800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:40696400-40697800	Active TSS	Liver	Liver
30	chr19:40696400-40697800	Active TSS	Right Ventricle	heart
31	chr19:40696400-40697800	Active TSS	Stomach Smooth Muscle	stomach
32	chr19:40696400-40698000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:40696400-40698000	Active TSS	Brain Cingulate Gyrus	brain
34	chr19:40696400-40698000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:40696400-40698000	Active TSS	Duodenum Mucosa	Duodenum
36	chr19:40696400-40698000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr19:40696400-40698000	Active TSS	Fetal Muscle Leg	muscle
38	chr19:40696400-40698000	Active TSS	Rectal Smooth Muscle	rectum
39	chr19:40696400-40698000	Active TSS	NH-A	brain
40	chr19:40696400-40698200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:40696400-40698200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr19:40696400-40698200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:40696400-40698200	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr19:40696400-40698200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr19:40696400-40698200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr19:40696400-40698200	Active TSS	Brain Substantia Nigra	brain
47	chr19:40696400-40698200	Active TSS	Ovary	ovary
48	chr19:40696400-40698200	Active TSS	Right Atrium	heart
49	chr19:40696400-40698200	Active TSS	HepG2	liver
50	chr19:40696400-40698200	Active TSS	NHDF-Ad	bronchial

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