Variant report

Variant	rs28565383
Chromosome Location	chr19:41879781-41879782
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	TCF12	chr19:41879718-41880403	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr19:41879745-41880395	SK-N-SH	brain:	n/a	n/a
3	RXRA	chr19:41879729-41880444	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr19:41879711-41879795	K562	blood:	n/a	n/a
5	POLR2A	chr19:41879774-41880295	SK-N-MC	brain:	n/a	n/a
6	TCF12	chr19:41879755-41880511	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr19:41879743-41880521	ECC-1	luminal epithelium:	n/a	n/a
8	RCOR1	chr19:41879670-41880473	IMR90	lung:	n/a	n/a
9	TCF12	chr19:41879623-41880568	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr19:41879731-41880497	SK-N-SH	brain:	n/a	n/a
11	NFIC	chr19:41879737-41880401	ECC-1	luminal epithelium:	n/a	chr19:41880110-41880126 chr19:41880078-41880106 chr19:41880110-41880127
12	TEAD4	chr19:41879763-41880344	SK-N-SH	brain:	n/a	n/a
13	ZNF263	chr19:41879743-41880247	HEK293-T-REx	kidney:	n/a	n/a
14	NFIC	chr19:41879666-41880502	ECC-1	luminal epithelium:	n/a	chr19:41880110-41880126 chr19:41880078-41880106 chr19:41880110-41880127
15	TCF12	chr19:41879711-41880466	A549	lung:	n/a	n/a
16	RXRA	chr19:41879760-41880347	SK-N-SH	brain:	n/a	n/a
17	SP1	chr19:41879747-41880351	A549	lung:	n/a	chr19:41879966-41879980
18	GATA3	chr19:41879744-41880518	SK-N-SH	brain:	n/a	n/a
19	PBX3	chr19:41879759-41880375	SK-N-SH	brain:	n/a	n/a
20	NFIC	chr19:41879734-41880433	SK-N-SH	brain:	n/a	chr19:41880110-41880126 chr19:41880078-41880106 chr19:41880110-41880127
21	EP300	chr19:41879755-41880386	SK-N-SH	brain:	n/a	chr19:41880366-41880380
22	EP300	chr19:41879774-41880387	ECC-1	luminal epithelium:	n/a	chr19:41880366-41880380
23	NFIC	chr19:41879732-41880530	SK-N-SH	brain:	n/a	chr19:41880110-41880126 chr19:41880078-41880106 chr19:41880110-41880127

No.	Distal block	Cell Line	Cell type
1	chr19:41877867..41880713-chr19:41901603..41903548,2	MCF-7	breast:
2	chr19:41868998..41873219-chr19:41877594..41880579,4	K562	blood:
3	chr19:41878956..41881468-chr19:41882311..41885014,3	K562	blood:
4	chr19:41869640..41871954-chr19:41878739..41881491,2	MCF-7	breast:
5	chr19:41872814..41874606-chr19:41878668..41881645,2	MCF-7	breast:
6	chr19:41878593..41880098-chr19:41880905..41883536,2	MCF-7	breast:
7	chr19:41858284..41860006-chr19:41877759..41881473,3	K562	blood:
8	chr19:41878619..41881645-chr19:41882135..41886243,4	MCF-7	breast:

Variant related genes	Relation type
BCKDHA	TF binding region
ENSG00000255730	TF binding region
TMEM91	TF binding region
ENSG00000077348	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000123810	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10408549	0.91[AFR][1000 genomes]
rs10418010	0.85[AFR][1000 genomes]
rs10424861	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41870600-41882000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:41870800-41882000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:41871000-41879800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:41871000-41879800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr19:41871000-41880000	Weak transcription	HSMMtube	muscle
6	chr19:41871000-41881800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:41871000-41882000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:41871000-41882000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:41871000-41882000	Weak transcription	Primary T cells from cord blood	blood
10	chr19:41871200-41879800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:41871200-41879800	Weak transcription	Brain Anterior Caudate	brain
12	chr19:41871200-41879800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:41871200-41879800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:41871200-41879800	Weak transcription	Fetal Lung	lung
15	chr19:41871200-41879800	Weak transcription	Left Ventricle	heart
16	chr19:41871200-41879800	Weak transcription	Right Ventricle	heart
17	chr19:41871200-41879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr19:41871200-41879800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:41871200-41880000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:41871200-41881800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr19:41871200-41882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:41871200-41882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:41871200-41882000	Weak transcription	Thymus	Thymus
24	chr19:41871200-41882200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:41871200-41884000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:41871200-41888600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:41871400-41882000	Weak transcription	Liver	Liver
28	chr19:41871400-41888400	Weak transcription	Dnd41	blood
29	chr19:41872400-41880000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:41872600-41881600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:41872600-41882200	Weak transcription	Fetal Thymus	thymus
32	chr19:41873000-41879800	Weak transcription	Lung	lung
33	chr19:41873800-41882000	Weak transcription	Spleen	Spleen
34	chr19:41874200-41879800	Weak transcription	Adipose Nuclei	Adipose
35	chr19:41874200-41879800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:41874200-41879800	Weak transcription	Gastric	stomach
37	chr19:41874200-41879800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:41874200-41881800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:41874200-41881800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:41874200-41882000	Weak transcription	Stomach Mucosa	stomach
41	chr19:41874200-41882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:41874400-41879800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:41874400-41882200	Weak transcription	Small Intestine	intestine
44	chr19:41874400-41882200	Weak transcription	HSMM	muscle
45	chr19:41874600-41879800	Weak transcription	NH-A	brain
46	chr19:41874600-41879800	Weak transcription	NHLF	lung
47	chr19:41874600-41880000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:41874800-41879800	Weak transcription	A549	lung
49	chr19:41874800-41879800	Weak transcription	HUVEC	blood vessel
50	chr19:41874800-41879800	Weak transcription	NHDF-Ad	bronchial

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