Variant report

Variant	rs142009673
Chromosome Location	chr19:42038260-42038261
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	PML	chr19:42037417-42038526	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:42035639-42038770	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:42035603-42038761	GM12892	blood:	n/a	n/a
4	FOS	chr19:42037865-42038275	MCF10A-Er-Src	breast:	n/a	chr19:42038013-42038022
5	GATA2	chr19:42036805-42038499	HUVEC	blood vessel:	n/a	chr19:42037364-42037378
6	MTA3	chr19:42037542-42038726	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:42037710-42038520	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:42035835-42038400	GM12892	blood:	n/a	n/a
9	SPI1	chr19:42037933-42038406	GM12891	blood:	n/a	chr19:42038186-42038199 chr19:42038185-42038198
10	BCLAF1	chr19:42037618-42038574	GM12878	blood:	n/a	n/a
11	JUND	chr19:42037799-42038429	K562	blood:	n/a	chr19:42038013-42038022
12	SPI1	chr19:42037894-42038376	GM12891	blood:	n/a	chr19:42038186-42038199 chr19:42038185-42038198
13	MAZ	chr19:42037832-42038345	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:42036966-42038325	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr19:42037347-42038286	GM12891	blood:	n/a	n/a
16	TAF1	chr19:42038026-42038302	PFSK-1	brain:	n/a	n/a
17	RUNX3	chr19:42037051-42038600	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:42037623-42038291	SK-N-MC	brain:	n/a	n/a
19	CEBPB	chr19:42038111-42038379	A549	lung:	n/a	n/a
20	PML	chr19:42037778-42038289	K562	blood:	n/a	n/a
21	POLR2A	chr19:42037642-42038624	GM12878	blood:	n/a	n/a
22	STAT3	chr19:42037877-42038359	MCF10A-Er-Src	breast:	n/a	chr19:42037983-42037995 chr19:42038234-42038245 chr19:42038233-42038247
23	SP1	chr19:42037766-42038266	GM12878	blood:	n/a	chr19:42037987-42037996 chr19:42038010-42038031 chr19:42037985-42037997
24	POLR2A	chr19:42037699-42038283	GM19099	blood:	n/a	n/a
25	E2F4	chr19:42037858-42038290	MCF10A-Er-Src	breast:	n/a	chr19:42037984-42037996
26	PML	chr19:42037733-42038275	GM12878	blood:	n/a	n/a
27	ATF2	chr19:42037562-42038519	GM12878	blood:	n/a	n/a
28	RCOR1	chr19:42037826-42038305	K562	blood:	n/a	n/a
29	POLR2A	chr19:42035831-42038634	GM18505	blood:	n/a	n/a
30	FOS	chr19:42037874-42038261	MCF10A-Er-Src	breast:	n/a	chr19:42038013-42038022
31	SPI1	chr19:42038012-42038315	K562	blood:	n/a	chr19:42038186-42038199 chr19:42038185-42038198
32	CEBPB	chr19:42038006-42038343	K562	blood:	n/a	n/a
33	SPI1	chr19:42038008-42038260	K562	blood:	n/a	chr19:42038186-42038199 chr19:42038185-42038198
34	SETDB1	chr19:42034208-42038482	U2OS	brain:	n/a	n/a
35	CREB1	chr19:42037640-42038535	GM12878	blood:	n/a	n/a
36	FOS	chr19:42036986-42038293	HUVEC	blood vessel:	n/a	chr19:42038013-42038022
37	MYC	chr19:42037975-42038360	MCF10A-Er-Src	breast:	n/a	n/a
38	RUNX3	chr19:42035847-42038620	GM12878	blood:	n/a	chr19:42036623-42036632 chr19:42036623-42036632
39	CREB1	chr19:42037728-42038519	GM12878	blood:	n/a	n/a
40	FOS	chr19:42037888-42038366	MCF10A-Er-Src	breast:	n/a	chr19:42038013-42038022
41	STAT3	chr19:42038100-42038378	MCF10A-Er-Src	breast:	n/a	chr19:42038234-42038245 chr19:42038233-42038247
42	STAT3	chr19:42038071-42038401	MCF10A-Er-Src	breast:	n/a	chr19:42038234-42038245 chr19:42038233-42038247
43	MEF2A	chr19:42037712-42038529	GM12878	blood:	n/a	chr19:42038215-42038236
44	ZNF263	chr19:42037435-42038280	HEK293-T-REx	kidney:	n/a	n/a
45	POLR2A	chr19:42036915-42038505	HUVEC	blood vessel:	n/a	n/a
46	FOS	chr19:42037803-42038318	MCF10A-Er-Src	breast:	n/a	chr19:42038013-42038022
47	SMC3	chr19:42038167-42038314	GM12878	blood:	n/a	n/a
48	STAT3	chr19:42037663-42038310	GM12878	blood:	n/a	chr19:42037983-42037995 chr19:42038234-42038245 chr19:42038233-42038247
49	FOXM1	chr19:42037643-42038486	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:42037557-42038404	HUVEC	blood vessel:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM21-3	chr19:42038230-42038534	ENSG00000268355.1

Variant related genes	Relation type
ENSG00000270164	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42035000-42038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:42036400-42038400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:42036600-42038800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:42036600-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:42036800-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:42036800-42039400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr19:42037000-42038600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr19:42037000-42038800	Enhancers	Fetal Muscle Leg	muscle
9	chr19:42037200-42038400	Weak transcription	Left Ventricle	heart
10	chr19:42037200-42038600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:42037200-42038800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr19:42037200-42042200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr19:42037400-42038400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr19:42037400-42038600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:42037400-42038800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr19:42037400-42038800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr19:42037600-42038400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:42037600-42038400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr19:42037600-42038400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr19:42037600-42038400	Flanking Bivalent TSS/Enh	A549	lung
21	chr19:42037600-42038600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:42037600-42038800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:42037800-42038400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:42037800-42038400	Active TSS	Thymus	Thymus
25	chr19:42037800-42038400	Enhancers	HUVEC	blood vessel
26	chr19:42037800-42038600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr19:42037800-42038600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:42037800-42038600	Enhancers	Esophagus	oesophagus
29	chr19:42037800-42038600	Flanking Active TSS	Fetal Lung	lung
30	chr19:42037800-42038600	Enhancers	Lung	lung
31	chr19:42037800-42038600	Active TSS	Rectal Smooth Muscle	rectum
32	chr19:42038000-42038400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:42038000-42038400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:42038000-42038400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:42038000-42038400	Enhancers	Colonic Mucosa	Colon
36	chr19:42038000-42038400	Active TSS	Duodenum Mucosa	Duodenum
37	chr19:42038000-42038400	Active TSS	Fetal Thymus	thymus
38	chr19:42038000-42038400	Active TSS	Right Atrium	heart
39	chr19:42038000-42038400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr19:42038000-42038400	Weak transcription	Spleen	Spleen
41	chr19:42038000-42038400	Flanking Active TSS	HMEC	breast
42	chr19:42038000-42038600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:42038000-42038600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:42038000-42038600	Active TSS	K562	blood
45	chr19:42038000-42038600	Bivalent Enhancer	Osteobl	bone
46	chr19:42038200-42038400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr19:42038200-42038400	Active TSS	Psoas Muscle	Psoas
48	chr19:42038200-42038400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:42038200-42038400	Active TSS	GM12878-XiMat	blood
50	chr19:42038200-42038400	Flanking Active TSS	Hela-S3	cervix

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