Variant report

Variant	rs28475392
Chromosome Location	chr19:19141696-19141697
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	chr19:19141631-19142026	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19140364..19142501-chr19:19142973..19144893,2	MCF-7	breast:

Variant related genes	Relation type
ARMC6	TF binding region
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10402411	0.90[AFR][1000 genomes]
rs10404020	0.90[AFR][1000 genomes]
rs10404879	0.83[AFR][1000 genomes]
rs10406282	0.83[AFR][1000 genomes]
rs10406341	0.83[AFR][1000 genomes]
rs10406496	0.86[AFR][1000 genomes]
rs10407260	0.83[AFR][1000 genomes]
rs10407753	0.86[AFR][1000 genomes]
rs10408567	0.86[AFR][1000 genomes]
rs10409265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409297	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409395	0.83[AFR][1000 genomes]
rs10412101	0.83[AFR][1000 genomes]
rs10414535	0.83[AFR][1000 genomes]
rs10414859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415998	0.95[AFR][1000 genomes]
rs10416041	0.83[AFR][1000 genomes]
rs10416054	0.83[AFR][1000 genomes]
rs10416240	0.83[AFR][1000 genomes]
rs10416250	0.83[AFR][1000 genomes]
rs10416730	0.83[AFR][1000 genomes]
rs10417310	0.83[AFR][1000 genomes]
rs10417682	0.83[AFR][1000 genomes]
rs10418688	0.83[AFR][1000 genomes]
rs10419114	0.83[AFR][1000 genomes]
rs10419307	0.83[AFR][1000 genomes]
rs10420559	0.86[AFR][1000 genomes]
rs10422058	0.83[AFR][1000 genomes]
rs10422079	0.81[AFR][1000 genomes]
rs10422238	0.90[AFR][1000 genomes]
rs10422813	0.81[AFR][1000 genomes]
rs10423129	0.83[AFR][1000 genomes]
rs10423504	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426131	0.83[AFR][1000 genomes]
rs13344835	0.95[AFR][1000 genomes]
rs13345246	0.83[AFR][1000 genomes]
rs28369262	0.86[AFR][1000 genomes]
rs28376498	0.88[AFR][1000 genomes]
rs28380085	0.81[AFR][1000 genomes]
rs28416794	0.95[AFR][1000 genomes]
rs28421315	0.83[AFR][1000 genomes]
rs28445835	0.88[AFR][1000 genomes]
rs28477157	0.83[AFR][1000 genomes]
rs28477961	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507927	0.83[AFR][1000 genomes]
rs28530647	0.90[AFR][1000 genomes]
rs28533991	0.92[AFR][1000 genomes]
rs28582808	0.81[AFR][1000 genomes]
rs28619464	0.88[AFR][1000 genomes]
rs28628081	0.83[AFR][1000 genomes]
rs28699197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28720008	0.83[AFR][1000 genomes]
rs35646935	0.83[AFR][1000 genomes]
rs6511012	0.81[AFR][1000 genomes]
rs7248183	1.00[AMR][1000 genomes]
rs7252085	0.81[AFR][1000 genomes]
rs7252172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8106189	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
5	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
8	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:19126400-19143400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:19126800-19142600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:19128000-19142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19128000-19142800	Strong transcription	Fetal Intestine Small	intestine
17	chr19:19128000-19142800	Weak transcription	Stomach Mucosa	stomach
18	chr19:19130200-19141800	Weak transcription	Fetal Heart	heart
19	chr19:19131200-19142000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:19131200-19142800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:19131400-19142400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:19132000-19142000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:19132200-19141800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:19132200-19142000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:19132400-19142400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:19132600-19141800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr19:19132600-19141800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr19:19132800-19142000	Strong transcription	Fetal Intestine Large	intestine
29	chr19:19133000-19141800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr19:19133000-19142600	Strong transcription	Lung	lung
31	chr19:19133200-19141800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:19133200-19141800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:19133200-19141800	Strong transcription	Brain Substantia Nigra	brain
34	chr19:19133200-19141800	Strong transcription	Fetal Lung	lung
35	chr19:19133200-19142000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:19133200-19142000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:19133200-19142000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:19133200-19142400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:19133400-19141800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:19133400-19142200	Strong transcription	NH-A	brain
41	chr19:19133600-19142000	Strong transcription	HUVEC	blood vessel
42	chr19:19133800-19141800	Weak transcription	Fetal Brain Male	brain
43	chr19:19134000-19141800	Strong transcription	Primary T cells from cord blood	blood
44	chr19:19134000-19142000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:19134200-19141800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:19134200-19141800	Strong transcription	Placenta	Placenta
47	chr19:19134200-19142000	Strong transcription	Thymus	Thymus
48	chr19:19134200-19142400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:19134400-19141800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:19134600-19142400	Strong transcription	Fetal Thymus	thymus

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