Variant report

Variant	rs61588415
Chromosome Location	chr3:28367913-28367914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28366029..28369870-chr3:28388937..28390962,3	K562	blood:

Variant related genes	Relation type
ENSG00000163512	Chromatin interaction
ENSG00000206559	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11916224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11918809	0.83[AMR][1000 genomes]
rs11919446	1.00[EUR][1000 genomes]
rs11923033	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11923748	1.00[EUR][1000 genomes]
rs11926821	1.00[EUR][1000 genomes]
rs55758484	1.00[EUR][1000 genomes]
rs55817728	1.00[EUR][1000 genomes]
rs55962685	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56082224	1.00[EUR][1000 genomes]
rs56199335	1.00[EUR][1000 genomes]
rs57400334	1.00[EUR][1000 genomes]
rs57850842	1.00[EUR][1000 genomes]
rs60023459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60355399	1.00[EUR][1000 genomes]
rs6794482	1.00[EUR][1000 genomes]
rs6800120	1.00[EUR][1000 genomes]
rs6800367	1.00[EUR][1000 genomes]
rs6804419	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73822335	0.83[AMR][1000 genomes]
rs73822569	0.85[AMR][1000 genomes]
rs73822571	0.85[AMR][1000 genomes]
rs73822575	0.85[AMR][1000 genomes]
rs73822579	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73822639	1.00[EUR][1000 genomes]
rs73822644	1.00[EUR][1000 genomes]
rs73822646	1.00[EUR][1000 genomes]
rs73822647	1.00[EUR][1000 genomes]
rs73823977	1.00[EUR][1000 genomes]
rs73823978	1.00[EUR][1000 genomes]
rs73823979	1.00[EUR][1000 genomes]
rs73823980	1.00[EUR][1000 genomes]
rs73823981	1.00[EUR][1000 genomes]
rs73823982	1.00[EUR][1000 genomes]
rs73823983	1.00[EUR][1000 genomes]
rs73823984	1.00[EUR][1000 genomes]
rs73823985	1.00[EUR][1000 genomes]
rs73823986	1.00[EUR][1000 genomes]
rs73823988	1.00[EUR][1000 genomes]
rs73825125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825141	0.90[AFR][1000 genomes]
rs73825145	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73825155	1.00[EUR][1000 genomes]
rs73825158	1.00[EUR][1000 genomes]
rs73825159	1.00[EUR][1000 genomes]
rs73825160	1.00[EUR][1000 genomes]
rs73825164	1.00[EUR][1000 genomes]
rs7627778	1.00[EUR][1000 genomes]
rs7628073	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649677	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
3	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
4	chr3:28349800-28389400	Weak transcription	Gastric	stomach
5	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:28356800-28376800	Weak transcription	Ovary	ovary
7	chr3:28357600-28370400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
9	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:28359600-28377200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:28360000-28368400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:28360200-28368200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr3:28360200-28368400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:28360400-28368400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:28360400-28383800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:28360600-28368000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:28361400-28368600	Strong transcription	Placenta	Placenta
19	chr3:28361600-28368000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:28361600-28368200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:28361600-28382200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:28362400-28368400	Strong transcription	Primary B cells from cord blood	blood
23	chr3:28362800-28368400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:28362800-28382400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
26	chr3:28363200-28377200	Weak transcription	Fetal Kidney	kidney
27	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:28363800-28380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
30	chr3:28364000-28368400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:28364000-28368400	Strong transcription	Fetal Lung	lung
32	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
33	chr3:28364200-28368400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:28364200-28368400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:28364200-28376800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:28364400-28368400	Strong transcription	NHDF-Ad	bronchial
37	chr3:28364400-28369000	Strong transcription	HSMM	muscle
38	chr3:28364400-28373200	Weak transcription	Brain Germinal Matrix	brain
39	chr3:28364600-28368000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:28364600-28368400	Strong transcription	Adipose Nuclei	Adipose
41	chr3:28364800-28368400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:28364800-28369000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:28364800-28377000	Weak transcription	Brain Substantia Nigra	brain
44	chr3:28364800-28382400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:28365000-28368200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:28365000-28368400	Strong transcription	Fetal Thymus	thymus
47	chr3:28365000-28368400	Strong transcription	Hela-S3	cervix
48	chr3:28365200-28368200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:28365200-28368200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:28365400-28368200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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