Variant report

Variant	rs73933647
Chromosome Location	chr19:42038452-42038453
allele	A/C
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	GATA2	chr19:42036805-42038499	HUVEC	blood vessel:	n/a	chr19:42037364-42037378
5	MTA3	chr19:42037542-42038726	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42037710-42038520	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:42038419-42038730	GM12892	blood:	n/a	n/a
8	BCLAF1	chr19:42037618-42038574	GM12878	blood:	n/a	n/a
9	RUNX3	chr19:42037051-42038600	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:42037642-42038624	GM12878	blood:	n/a	n/a
11	ATF2	chr19:42037562-42038519	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:42035831-42038634	GM18505	blood:	n/a	n/a
13	YY1	chr19:42038340-42038644	GM12892	blood:	n/a	n/a
14	SETDB1	chr19:42034208-42038482	U2OS	brain:	n/a	n/a
15	CREB1	chr19:42037640-42038535	GM12878	blood:	n/a	n/a
16	RUNX3	chr19:42035847-42038620	GM12878	blood:	n/a	chr19:42036623-42036632 chr19:42036623-42036632
17	CREB1	chr19:42037728-42038519	GM12878	blood:	n/a	n/a
18	MEF2A	chr19:42037712-42038529	GM12878	blood:	n/a	chr19:42038215-42038236
19	POLR2A	chr19:42036915-42038505	HUVEC	blood vessel:	n/a	n/a
20	FOXM1	chr19:42037643-42038486	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:42035515-42038686	GM12891	blood:	n/a	n/a
22	POLR2A	chr19:42035667-42038718	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:42038394-42038713	GM12892	blood:	n/a	n/a
24	SPI1	chr19:42037770-42038761	HL-60	blood:	n/a	chr19:42038186-42038199 chr19:42038185-42038198 chr19:42038646-42038659
25	POLR2A	chr19:42036976-42038544	HL-60	blood:	n/a	n/a
26	NFIC	chr19:42037725-42038546	GM12878	blood:	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: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12327737	1.00[EUR][1000 genomes]
rs55777535	1.00[EUR][1000 genomes]
rs55786333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030121	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58563692	1.00[EUR][1000 genomes]
rs59823881	1.00[EUR][1000 genomes]
rs60118562	1.00[EUR][1000 genomes]
rs7251392	1.00[AFR][1000 genomes]
rs73560846	1.00[EUR][1000 genomes]
rs73931484	1.00[AMR][1000 genomes]
rs73931497	1.00[EUR][1000 genomes]
rs73931501	1.00[EUR][1000 genomes]
rs73931502	1.00[EUR][1000 genomes]
rs73933641	1.00[EUR][1000 genomes]
rs73933645	1.00[AFR][1000 genomes]
rs9973242	1.00[EUR][1000 genomes]

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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42036600-42038800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42036600-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:42036800-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:42036800-42039400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:42037000-42038600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr19:42037000-42038800	Enhancers	Fetal Muscle Leg	muscle
7	chr19:42037200-42038600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:42037200-42038800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr19:42037200-42042200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr19:42037400-42038600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:42037400-42038800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:42037400-42038800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr19:42037600-42038600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:42037600-42038800	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr19:42037800-42038600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr19:42037800-42038600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:42037800-42038600	Enhancers	Esophagus	oesophagus
18	chr19:42037800-42038600	Flanking Active TSS	Fetal Lung	lung
19	chr19:42037800-42038600	Enhancers	Lung	lung
20	chr19:42037800-42038600	Active TSS	Rectal Smooth Muscle	rectum
21	chr19:42038000-42038600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:42038000-42038600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:42038000-42038600	Active TSS	K562	blood
24	chr19:42038000-42038600	Bivalent Enhancer	Osteobl	bone
25	chr19:42038200-42038600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:42038200-42038600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:42038200-42038600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr19:42038200-42038600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:42038200-42038600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:42038200-42038600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:42038200-42038600	Active TSS	Brain Hippocampus Middle	brain
32	chr19:42038200-42038600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr19:42038200-42038600	Enhancers	Stomach Mucosa	stomach
34	chr19:42038200-42038600	Flanking Bivalent TSS/Enh	HSMMtube	muscle
35	chr19:42038200-42038800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:42038200-42038800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr19:42038200-42038800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:42038200-42039000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr19:42038400-42038600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:42038400-42038600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:42038400-42038600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:42038400-42038600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:42038400-42038600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:42038400-42038600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:42038400-42038600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:42038400-42038600	Flanking Active TSS	Colonic Mucosa	Colon
47	chr19:42038400-42038600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr19:42038400-42038600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
49	chr19:42038400-42038600	Enhancers	Left Ventricle	heart
50	chr19:42038400-42038600	Flanking Active TSS	Psoas Muscle	Psoas

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