Variant report

Variant	rs28582808
Chromosome Location	chr19:19157106-19157107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19152497..19156413-chr19:19157001..19159635,3	K562	blood:
2	chr19:19155234..19157690-chr19:19163937..19165951,2	K562	blood:
3	chr19:19155401..19157950-chr19:19174734..19177618,2	K562	blood:

Variant related genes	Relation type
ENSG00000181035	Chromatin interaction
ENSG00000105676	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10402411	0.82[AFR][1000 genomes]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407980	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409297	0.86[AFR][1000 genomes]
rs10409395	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414859	0.86[AFR][1000 genomes]
rs10416041	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422238	0.82[AFR][1000 genomes]
rs10422813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423504	0.84[AFR][1000 genomes]
rs10426131	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13345246	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28416794	0.86[AFR][1000 genomes]
rs28421315	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28475392	0.81[AFR][1000 genomes]
rs28477157	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	0.88[AFR][1000 genomes]
rs28507927	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28530647	0.82[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28619464	0.93[AFR][1000 genomes]
rs28628081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28699197	0.81[AFR][1000 genomes]
rs28720008	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252172	0.88[AFR][1000 genomes]
rs7256152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106189	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917000	1.00[EUR][1000 genomes]
rs9917034	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19145000-19174000	Weak transcription	Small Intestine	intestine
2	chr19:19145400-19165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:19145400-19171800	Weak transcription	Right Atrium	heart
4	chr19:19145600-19159600	Weak transcription	NH-A	brain
5	chr19:19145600-19172200	Weak transcription	Stomach Mucosa	stomach
6	chr19:19145600-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:19145600-19173800	Weak transcription	Fetal Kidney	kidney
8	chr19:19146600-19161800	Weak transcription	Psoas Muscle	Psoas
9	chr19:19148400-19161600	Weak transcription	Fetal Heart	heart
10	chr19:19149400-19164800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:19151000-19173800	Weak transcription	Fetal Brain Male	brain
12	chr19:19151200-19158000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:19151400-19162000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:19151800-19166000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:19151800-19173800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:19151800-19173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:19152600-19173200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:19152800-19161000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:19152800-19171400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:19153200-19158800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:19153200-19158800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:19153200-19158800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:19153200-19158800	Strong transcription	Thymus	Thymus
24	chr19:19153200-19159000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:19153200-19160000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:19153200-19171000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr19:19153200-19171200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:19153200-19171400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:19153200-19172200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:19153200-19173600	Strong transcription	Fetal Stomach	stomach
31	chr19:19153400-19157400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:19153400-19158400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:19153400-19158800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:19153400-19158800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr19:19153400-19158800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:19153400-19159000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr19:19153400-19159000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:19153400-19163800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:19153400-19167400	Strong transcription	Fetal Muscle Leg	muscle
40	chr19:19153400-19168400	Strong transcription	Fetal Intestine Small	intestine
41	chr19:19153400-19168600	Strong transcription	Fetal Intestine Large	intestine
42	chr19:19153400-19169800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:19153400-19170400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr19:19153400-19170800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:19153400-19170800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:19153400-19170800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:19153400-19171000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:19153400-19171200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:19153600-19158400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19153600-19158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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