Variant report

Variant	rs10405178
Chromosome Location	chr19:19175752-19175753
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19172859..19177096-chr19:19213191..19220004,7	K562	blood:
2	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
3	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
4	chr1:76250892..76253394-chr19:19175061..19177790,2	K562	blood:
5	chr19:19170341..19177029-chr19:19229928..19235464,11	K562	blood:
6	chr19:19170465..19178046-chr19:19213939..19220242,15	K562	blood:
7	chr19:19143657..19146284-chr19:19174594..19176382,2	MCF-7	breast:
8	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
9	chr19:19169419..19177029-chr19:19229685..19233171,13	K562	blood:
10	chr19:19141992..19145825-chr19:19171077..19177701,15	K562	blood:
11	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:

No data

Variant related genes	Relation type
ENSG00000206620	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000181035	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10402411	0.89[AFR][1000 genomes]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409297	0.84[AFR][1000 genomes]
rs10409395	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414859	0.84[AFR][1000 genomes]
rs10416041	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423504	0.86[AFR][1000 genomes]
rs10426131	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13345246	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28416794	0.84[AFR][1000 genomes]
rs28421315	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477157	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	0.86[AFR][1000 genomes]
rs28507927	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28530647	0.84[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.91[AFR][1000 genomes]
rs28628081	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28720008	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7247645	1.00[EUR][1000 genomes]
rs7248183	1.00[YRI][hapmap]
rs7252085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252172	0.82[AFR][1000 genomes]
rs7256152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106189	0.86[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:5 , 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
4	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv17267	chr19:19174047-19177125	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 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	chr19:19174000-19176200	Active TSS	Gastric	stomach
2	chr19:19174000-19176200	Active TSS	Ovary	ovary
3	chr19:19174000-19176400	Active TSS	Fetal Kidney	kidney
4	chr19:19174000-19176400	Active TSS	Right Atrium	heart
5	chr19:19174000-19176600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:19174000-19176600	Active TSS	Thymus	Thymus
7	chr19:19174200-19175800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:19174200-19175800	Active TSS	Left Ventricle	heart
9	chr19:19174200-19175800	Active TSS	A549	lung
10	chr19:19174200-19175800	Active TSS	HSMMtube	muscle
11	chr19:19174200-19176000	Active TSS	HepG2	liver
12	chr19:19174200-19176200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:19174200-19176200	Active TSS	Small Intestine	intestine
14	chr19:19174200-19176400	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr19:19174200-19176400	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr19:19174800-19176400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr19:19175000-19175800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:19175000-19175800	Flanking Active TSS	Spleen	Spleen
19	chr19:19175000-19176000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:19175000-19176000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr19:19175000-19176200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:19175000-19176200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr19:19175000-19176200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr19:19175000-19176200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr19:19175000-19176200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:19175000-19176200	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr19:19175000-19176200	Flanking Active TSS	Placenta	Placenta
28	chr19:19175000-19176400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr19:19175000-19176400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:19175000-19176400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr19:19175000-19176400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:19175000-19176400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:19175000-19176400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:19175000-19176400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:19175000-19176400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:19175000-19176400	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr19:19175000-19176400	Flanking Active TSS	Colonic Mucosa	Colon
38	chr19:19175000-19176400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr19:19175000-19176400	Flanking Active TSS	Right Ventricle	heart
40	chr19:19175000-19176400	Flanking Active TSS	Dnd41	blood
41	chr19:19175000-19176400	Flanking Active TSS	HMEC	breast
42	chr19:19175000-19176400	Flanking Active TSS	HUVEC	blood vessel
43	chr19:19175000-19176400	Flanking Active TSS	Osteobl	bone
44	chr19:19175000-19176600	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr19:19175000-19176600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:19175000-19176600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:19175000-19176600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19175000-19176600	Flanking Active TSS	Liver	Liver
49	chr19:19175000-19176600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr19:19175000-19177200	Flanking Active TSS	Primary B cells from cord blood	blood

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