Variant report

Variant	rs28679850
Chromosome Location	chr19:40917651-40917652
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	EBF1	chr19:40917449-40917773	GM12878	blood:	n/a	n/a
2	NR3C1	chr19:40917364-40917838	A549	lung:	n/a	chr19:40917619-40917633 chr19:40917619-40917633 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634
3	EBF1	chr19:40916824-40917821	GM12878	blood:	n/a	n/a
4	NR3C1	chr19:40917225-40917853	A549	lung:	n/a	chr19:40917619-40917633 chr19:40917619-40917633 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634
5	NR3C1	chr19:40917287-40917823	A549	lung:	n/a	chr19:40917619-40917633 chr19:40917619-40917633 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634
6	POLR2A	chr19:40916173-40917856	K562	blood:	n/a	n/a
7	NR3C1	chr19:40917331-40917709	A549	lung:	n/a	chr19:40917619-40917633 chr19:40917619-40917633 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634
8	MTA3	chr19:40916650-40917791	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:40917060-40917677	HCT-116	colon:	n/a	n/a
10	POLR2A	chr19:40917152-40917728	HCT-116	colon:	n/a	n/a
11	NR3C1	chr19:40917387-40917696	A549	lung:	n/a	chr19:40917619-40917633 chr19:40917619-40917633 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634 chr19:40917618-40917634

No.	Distal block	Cell Line	Cell type
1	chr19:40914819..40917676-chr19:40926759..40928384,2	MCF-7	breast:
2	chr19:40911341..40916843-chr19:40917541..40922029,6	MCF-7	breast:
3	chr19:40916047..40918713-chr19:40928638..40931104,2	MCF-7	breast:
4	chr19:40908607..40910683-chr19:40915791..40917984,2	MCF-7	breast:
5	chr19:40877108..40878851-chr19:40916011..40918200,2	K562	blood:

Variant related genes	Relation type
PRX	TF binding region
ENSG00000105227	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10408405	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412156	1.00[EUR][1000 genomes]
rs10422945	1.00[EUR][1000 genomes]
rs10424704	1.00[EUR][1000 genomes]
rs11879375	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345497	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346024	1.00[EUR][1000 genomes]
rs268659	1.00[EUR][1000 genomes]
rs28407044	1.00[EUR][1000 genomes]
rs28728269	1.00[EUR][1000 genomes]
rs3730257	1.00[EUR][1000 genomes]
rs4150984	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55646097	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55860305	1.00[EUR][1000 genomes]
rs55954198	1.00[EUR][1000 genomes]
rs59129285	1.00[EUR][1000 genomes]
rs60115762	1.00[EUR][1000 genomes]
rs61018633	1.00[EUR][1000 genomes]
rs73559625	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559626	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73933256	1.00[EUR][1000 genomes]
rs73933258	1.00[EUR][1000 genomes]
rs73933265	1.00[EUR][1000 genomes]
rs73933270	1.00[EUR][1000 genomes]
rs73933276	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40910200-40919000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr19:40910200-40926800	Weak transcription	Gastric	stomach
3	chr19:40910600-40918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:40910600-40921000	Weak transcription	Fetal Kidney	kidney
5	chr19:40910600-40922800	Weak transcription	Fetal Thymus	thymus
6	chr19:40914200-40919400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:40914400-40922800	Weak transcription	Colonic Mucosa	Colon
8	chr19:40914400-40926600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:40915400-40923000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:40915600-40918400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:40915600-40918400	Enhancers	Spleen	Spleen
12	chr19:40915600-40919000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr19:40915600-40919200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:40915800-40918000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:40915800-40918200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr19:40915800-40918200	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:40916000-40919200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:40916200-40919000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:40916200-40919000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:40916400-40918000	Enhancers	Fetal Muscle Trunk	muscle
21	chr19:40916600-40917800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:40916600-40917800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:40916600-40920200	Enhancers	Primary hematopoietic stem cells	blood
24	chr19:40916800-40917800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr19:40916800-40918000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr19:40916800-40918200	Enhancers	Right Atrium	heart
27	chr19:40916800-40918400	Enhancers	Fetal Heart	heart
28	chr19:40916800-40918800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr19:40916800-40919000	Enhancers	Fetal Muscle Leg	muscle
30	chr19:40916800-40919800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:40916800-40921000	Enhancers	Right Ventricle	heart
32	chr19:40917000-40917800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:40917000-40918000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:40917000-40918000	Enhancers	Duodenum Mucosa	Duodenum
35	chr19:40917000-40918000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr19:40917000-40918000	Enhancers	A549	lung
37	chr19:40917000-40918200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:40917000-40918200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:40917000-40918200	Enhancers	Placenta	Placenta
40	chr19:40917000-40918200	Enhancers	Hela-S3	cervix
41	chr19:40917000-40918200	Enhancers	HMEC	breast
42	chr19:40917000-40918200	Enhancers	NHEK	skin
43	chr19:40917000-40918400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:40917000-40918400	Enhancers	Fetal Intestine Large	intestine
45	chr19:40917000-40918800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr19:40917000-40919200	Enhancers	Fetal Intestine Small	intestine
47	chr19:40917000-40919400	Enhancers	Left Ventricle	heart
48	chr19:40917000-40920000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:40917200-40918000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:40917200-40918000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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