Variant report

Variant	rs28412019
Chromosome Location	chr8:54868498-54868499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:54864473..54868508-chr8:54874228..54876255,3	K562	blood:
2	chr8:54866574..54869631-chr8:54872267..54874900,3	MCF-7	breast:
3	chr8:54849613..54851701-chr8:54866654..54869224,2	K562	blood:
4	chr8:54867998..54869976-chr8:54891193..54893956,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10093311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10093431	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10095163	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10095164	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10095679	0.86[EUR][1000 genomes]
rs10096376	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10099080	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10101289	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10102439	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10102726	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10102905	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10112203	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1044604	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1112697	0.82[AMR][1000 genomes]
rs1112698	0.82[AMR][1000 genomes]
rs11986605	0.86[AMR][1000 genomes]
rs11988830	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11988859	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11993180	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11994366	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11998000	0.82[AMR][1000 genomes]
rs11998659	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16919750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16919924	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28369337	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28379732	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28397021	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28413072	0.87[AMR][1000 genomes]
rs28431894	0.86[EUR][1000 genomes]
rs28507589	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28565202	1.00[EUR][1000 genomes]
rs28707072	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28736685	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28759114	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55704212	0.82[AMR][1000 genomes]
rs55781183	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55864901	0.82[AMR][1000 genomes]
rs56087054	0.82[AMR][1000 genomes]
rs56902942	1.00[EUR][1000 genomes]
rs57093383	0.82[AMR][1000 genomes]
rs58515879	0.82[AMR][1000 genomes]
rs58595525	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59087284	0.82[AMR][1000 genomes]
rs59114404	0.82[AMR][1000 genomes]
rs59277432	0.82[AMR][1000 genomes]
rs59387379	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60186893	0.82[AMR][1000 genomes]
rs60672236	0.80[EUR][1000 genomes]
rs60805450	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6473899	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6473901	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6473902	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6473903	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6473905	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6473906	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6473907	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6473908	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6981386	0.82[AMR][1000 genomes]
rs6983650	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6983958	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6984119	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6989211	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6992073	0.82[AMR][1000 genomes]
rs7001391	0.82[AMR][1000 genomes]
rs7003793	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7004808	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7005653	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7007028	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7007031	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7007176	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7008593	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7014036	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7016108	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7018089	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7018355	1.00[EUR][1000 genomes]
rs73589273	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73589277	0.86[EUR][1000 genomes]
rs73589286	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73589295	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73590817	0.93[EUR][1000 genomes]
rs73679588	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73679589	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73679596	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73679602	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73681304	0.87[EUR][1000 genomes]
rs73681305	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73681307	0.82[AMR][1000 genomes]
rs73681308	0.82[AMR][1000 genomes]
rs73681309	0.82[AMR][1000 genomes]
rs73681805	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73681806	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7815998	0.82[AMR][1000 genomes]
rs7822750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7823234	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7824355	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7824979	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7833336	0.82[AMR][1000 genomes]
rs7834757	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7836760	0.82[AMR][1000 genomes]
rs7844291	0.82[AMR][1000 genomes]
rs7844299	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7844390	0.86[EUR][1000 genomes]
rs7846650	1.00[EUR][1000 genomes]
rs9771960	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	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription 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 lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2758160	chr8:54832990-55016965	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759617	chr8:54832990-55016965	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv427821	chr8:54832990-55016965	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54851200-54872600	Weak transcription	Brain Germinal Matrix	brain
2	chr8:54852200-54872600	Weak transcription	Fetal Brain Female	brain
3	chr8:54852400-54872600	Weak transcription	Esophagus	oesophagus
4	chr8:54853800-54869000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:54856400-54889400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:54858000-54870800	Weak transcription	Brain Anterior Caudate	brain
7	chr8:54858000-54870800	Weak transcription	Fetal Muscle Leg	muscle
8	chr8:54858000-54871400	Weak transcription	Primary B cells from cord blood	blood
9	chr8:54858000-54872000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:54858200-54872200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr8:54858200-54872600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:54858200-54872600	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:54858200-54879000	Weak transcription	Right Atrium	heart
14	chr8:54858400-54871400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr8:54858400-54872600	Weak transcription	Lung	lung
16	chr8:54859000-54872200	Weak transcription	Aorta	Aorta
17	chr8:54859600-54869400	Weak transcription	HMEC	breast
18	chr8:54859600-54881200	Weak transcription	Hela-S3	cervix
19	chr8:54859600-54885400	Weak transcription	K562	blood
20	chr8:54862000-54879200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:54862200-54872200	Weak transcription	Primary T cells from cord blood	blood
22	chr8:54862200-54879200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:54864000-54868600	Weak transcription	NHEK	skin
24	chr8:54865800-54868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:54866000-54869600	Weak transcription	Placenta	Placenta
26	chr8:54866000-54872000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr8:54866200-54870000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:54866200-54870000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr8:54866200-54872600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:54866400-54872000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:54866600-54872600	Weak transcription	Fetal Lung	lung
32	chr8:54866600-54872600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:54866600-54872600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr8:54866600-54873400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr8:54866600-54893600	Weak transcription	Fetal Kidney	kidney
36	chr8:54866800-54870000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:54866800-54872000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr8:54866800-54872200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:54866800-54872600	Weak transcription	Fetal Stomach	stomach
40	chr8:54866800-54872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:54866800-54873200	Weak transcription	Ovary	ovary
42	chr8:54866800-54875400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:54866800-54885200	Weak transcription	NH-A	brain
44	chr8:54866800-54898000	Weak transcription	Colon Smooth Muscle	Colon
45	chr8:54866800-54898200	Weak transcription	Fetal Heart	heart
46	chr8:54867000-54868600	Weak transcription	NHLF	lung
47	chr8:54867000-54868800	Weak transcription	A549	lung
48	chr8:54867000-54870600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr8:54867000-54870800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr8:54867000-54871400	Weak transcription	NHDF-Ad	bronchial

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