Variant report

Variant	rs10405609
Chromosome Location	chr19:19177809-19177810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19176303..19177932-chr19:19191338..19193529,2	K562	blood:
2	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
3	chr19:19174780..19176762-chr19:19177154..19178760,2	MCF-7	breast:
4	chr19:19170465..19178046-chr19:19213939..19220242,15	K562	blood:
5	chr19:19176990..19179338-chr19:19181628..19184971,3	K562	blood:

Variant related genes	Relation type
ENSG00000181035	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10402411	0.85[AFR][1000 genomes]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409297	0.80[AFR][1000 genomes]
rs10409395	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414859	0.80[AFR][1000 genomes]
rs10416041	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	1.00[EUR][1000 genomes]
rs10418688	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	1.00[EUR][1000 genomes]
rs10420559	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422813	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423504	0.83[AFR][1000 genomes]
rs10426131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13345246	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28416794	0.80[AFR][1000 genomes]
rs28421315	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477157	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	0.83[AFR][1000 genomes]
rs28507927	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28530647	0.80[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.87[AFR][1000 genomes]
rs28628081	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28720008	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7247645	1.00[EUR][1000 genomes]
rs7252085	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7256152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106189	0.83[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:4 , 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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19175400-19207800	Weak transcription	Aorta	Aorta
2	chr19:19176000-19184600	Weak transcription	Spleen	Spleen
3	chr19:19176200-19185800	Weak transcription	Ovary	ovary
4	chr19:19176200-19186000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:19176400-19178000	Weak transcription	Brain Substantia Nigra	brain
6	chr19:19176400-19178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:19176400-19178400	Enhancers	HepG2	liver
8	chr19:19176400-19178800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr19:19176400-19179400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr19:19176400-19179800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:19176400-19179800	Weak transcription	Brain Germinal Matrix	brain
12	chr19:19176400-19179800	Weak transcription	Placenta	Placenta
13	chr19:19176400-19180000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:19176400-19180000	Weak transcription	Brain Anterior Caudate	brain
15	chr19:19176400-19180000	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:19176400-19180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:19176400-19180000	Weak transcription	Left Ventricle	heart
18	chr19:19176400-19180000	Weak transcription	Lung	lung
19	chr19:19176400-19180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:19176400-19180600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:19176400-19181200	Weak transcription	Fetal Intestine Small	intestine
22	chr19:19176400-19182000	Weak transcription	Small Intestine	intestine
23	chr19:19176400-19183600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:19176400-19186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:19176400-19189200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:19176400-19190400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:19176400-19190600	Weak transcription	Esophagus	oesophagus
28	chr19:19176400-19192600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:19176400-19192600	Weak transcription	Right Atrium	heart
30	chr19:19176400-19215200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:19176400-19215800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:19176400-19215800	Weak transcription	NHLF	lung
33	chr19:19176600-19178000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:19176600-19178000	Enhancers	Primary T cells from cord blood	blood
35	chr19:19176600-19178000	Weak transcription	Brain Angular Gyrus	brain
36	chr19:19176600-19178000	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:19176600-19178000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr19:19176600-19178000	Enhancers	Fetal Thymus	thymus
39	chr19:19176600-19178200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr19:19176600-19178400	Weak transcription	HSMMtube	muscle
41	chr19:19176600-19178600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr19:19176600-19178800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:19176600-19178800	Enhancers	K562	blood
44	chr19:19176600-19179600	Weak transcription	Right Ventricle	heart
45	chr19:19176600-19179800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr19:19176600-19179800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:19176600-19179800	Weak transcription	Fetal Stomach	stomach
48	chr19:19176600-19179800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr19:19176600-19180000	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:19176600-19180000	Enhancers	Primary T cells fromperipheralblood	blood

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