Variant report

Variant	rs10408525
Chromosome Location	chr19:55911712-55911713
allele	A/G
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55910368..55912840-chr19:55964651..55967610,2	K562	blood:
2	chr19:55911623..55913706-chr19:55914461..55917038,2	MCF-7	breast:
3	chr19:55911367..55913938-chr19:55973377..55976304,2	K562	blood:
4	chr17:39845023..39845572-chr19:55911408..55912116,2	HCT-116	colon:
5	chr19:55769482..55772014-chr19:55910008..55913343,3	K562	blood:
6	chr19:55910844..55913006-chr19:55952542..55954951,2	K562	blood:
7	chr19:55909744..55913358-chr19:55997717..56001739,3	K562	blood:
8	chr19:55789731..55792765-chr19:55910242..55912226,3	K562	blood:
9	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2S-1	chr19:55911113-55911787	ENSG00000267093.1

No data

Variant related genes	Relation type
ENSG00000105063	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179954	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10403564	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407066	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408540	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411984	0.83[AFR][1000 genomes]
rs10415365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416908	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420818	0.95[AFR][1000 genomes]
rs10421889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424289	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425362	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425596	0.83[AFR][1000 genomes]
rs28408730	0.95[AFR][1000 genomes]
rs28536711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59698058	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617871	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617888	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617896	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619651	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55899200-55913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
3	chr19:55900400-55911800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
5	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
6	chr19:55901200-55913200	Weak transcription	Small Intestine	intestine
7	chr19:55901400-55912000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:55901600-55911800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:55901600-55911800	Weak transcription	HUVEC	blood vessel
10	chr19:55901600-55912000	Weak transcription	HSMM	muscle
11	chr19:55901600-55914400	Weak transcription	Fetal Kidney	kidney
12	chr19:55901800-55911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:55901800-55911800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
15	chr19:55902000-55911800	Weak transcription	Ovary	ovary
16	chr19:55902000-55912200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:55902200-55911800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:55902200-55912400	Weak transcription	Colonic Mucosa	Colon
19	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:55902400-55912000	Weak transcription	Aorta	Aorta
21	chr19:55902600-55911800	Weak transcription	HMEC	breast
22	chr19:55903000-55911800	Weak transcription	Brain Substantia Nigra	brain
23	chr19:55903000-55911800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:55903000-55911800	Weak transcription	NHDF-Ad	bronchial
25	chr19:55903000-55912000	Weak transcription	Brain Angular Gyrus	brain
26	chr19:55903000-55912000	Weak transcription	Gastric	stomach
27	chr19:55903000-55912000	Weak transcription	Pancreas	Pancrea
28	chr19:55903000-55913200	Weak transcription	Fetal Lung	lung
29	chr19:55903000-55914000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr19:55903200-55911800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:55903200-55911800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:55903200-55911800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:55903400-55911800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:55903400-55911800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:55903400-55911800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:55903400-55911800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:55903400-55911800	Weak transcription	Right Ventricle	heart
38	chr19:55903400-55911800	Weak transcription	NHEK	skin
39	chr19:55903400-55911800	Weak transcription	NHLF	lung
40	chr19:55903400-55912000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:55903400-55913000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:55903400-55913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:55903600-55911800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:55903600-55911800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:55903600-55912200	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:55903800-55911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:55903800-55911800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:55903800-55911800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:55903800-55911800	Weak transcription	Adipose Nuclei	Adipose
50	chr19:55903800-55911800	Weak transcription	Liver	Liver

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