Variant report

Variant	rs10420559
Chromosome Location	chr19:19149850-19149851
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19143762..19145287-chr19:19149753..19152112,2	K562	blood:
2	chr19:19147736..19150233-chr19:19170434..19173422,2	K562	blood:
3	chr19:19148470..19151421-chr19:19152094..19154668,2	K562	blood:
4	chr19:19142730..19148953-chr19:19149447..19156213,13	K562	blood:
5	chr19:19148387..19150920-chr19:19203551..19206895,3	K562	blood:
6	chr19:19146038..19148163-chr19:19149447..19151209,2	K562	blood:
7	chr19:19148010..19150242-chr19:19312371..19314078,2	K562	blood:
8	chr19:19133809..19135508-chr19:19148686..19150405,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184162	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404020	0.84[YRI][hapmap]
rs10404077	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407980	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409265	0.82[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10409297	0.81[AFR][1000 genomes]
rs10409395	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10411413	1.00[YRI][hapmap]
rs10411786	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414859	0.81[AFR][1000 genomes]
rs10415998	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10416041	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422238	0.86[AFR][1000 genomes]
rs10422813	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426131	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13344835	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs13345246	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28416794	0.81[AFR][1000 genomes]
rs28421315	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28475392	0.86[AFR][1000 genomes]
rs28477157	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	0.93[AFR][1000 genomes]
rs28507927	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.98[AFR][1000 genomes]
rs28628081	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28699197	0.82[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs28720008	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2872205	1.00[MEX][hapmap]
rs35646935	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248183	1.00[MEX][hapmap]
rs7252085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252172	0.84[AFR][1000 genomes]
rs7256152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106189	0.92[YRI][hapmap];0.93[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	chr19:19145000-19154800	Weak transcription	Aorta	Aorta
2	chr19:19145000-19174000	Weak transcription	Small Intestine	intestine
3	chr19:19145200-19153600	Weak transcription	Ovary	ovary
4	chr19:19145400-19153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:19145400-19165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:19145400-19171800	Weak transcription	Right Atrium	heart
7	chr19:19145600-19150000	Weak transcription	NHLF	lung
8	chr19:19145600-19150200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:19145600-19150200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:19145600-19150200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:19145600-19150600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:19145600-19151000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:19145600-19151400	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:19145600-19151400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr19:19145600-19151600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:19145600-19153200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:19145600-19153400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:19145600-19153400	Weak transcription	Brain Substantia Nigra	brain
19	chr19:19145600-19153400	Weak transcription	Colonic Mucosa	Colon
20	chr19:19145600-19153400	Weak transcription	Gastric	stomach
21	chr19:19145600-19153400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:19145600-19153600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:19145600-19153600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:19145600-19153600	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:19145600-19153600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:19145600-19153600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:19145600-19153800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:19145600-19154000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:19145600-19154600	Weak transcription	HUVEC	blood vessel
30	chr19:19145600-19154600	Weak transcription	NHDF-Ad	bronchial
31	chr19:19145600-19154800	Weak transcription	Brain Angular Gyrus	brain
32	chr19:19145600-19154800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:19145600-19159600	Weak transcription	NH-A	brain
34	chr19:19145600-19172200	Weak transcription	Stomach Mucosa	stomach
35	chr19:19145600-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:19145600-19173800	Weak transcription	Fetal Kidney	kidney
37	chr19:19145800-19150000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:19145800-19150200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr19:19145800-19150200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:19145800-19153400	Weak transcription	Spleen	Spleen
41	chr19:19146200-19150200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:19146200-19150400	Strong transcription	Fetal Stomach	stomach
43	chr19:19146200-19151600	Weak transcription	Adipose Nuclei	Adipose
44	chr19:19146200-19153600	Weak transcription	Right Ventricle	heart
45	chr19:19146200-19154000	Weak transcription	Left Ventricle	heart
46	chr19:19146400-19150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:19146400-19150200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:19146400-19150400	Weak transcription	Fetal Brain Male	brain
49	chr19:19146400-19150400	Weak transcription	HepG2	liver
50	chr19:19146400-19150600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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