Variant report

Variant	rs28546170
Chromosome Location	chr5:80905638-80905639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10036942	1.00[ASN][1000 genomes]
rs10050981	1.00[ASN][1000 genomes]
rs10053226	0.81[EUR][1000 genomes]
rs10054360	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056236	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10057707	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10059425	0.90[EUR][1000 genomes]
rs10060208	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060828	0.89[ASN][1000 genomes]
rs10062494	0.90[EUR][1000 genomes]
rs10064862	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10064938	0.90[EUR][1000 genomes]
rs10066110	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10069094	0.97[AFR][1000 genomes]
rs10074416	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10074423	0.81[EUR][1000 genomes]
rs10078696	0.81[EUR][1000 genomes]
rs10473849	0.89[ASN][1000 genomes]
rs10473850	0.90[EUR][1000 genomes]
rs10474032	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10474033	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10474035	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942268	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10942277	0.90[EUR][1000 genomes]
rs10942278	0.90[EUR][1000 genomes]
rs10942279	0.90[EUR][1000 genomes]
rs13354281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357855	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13359852	0.81[EUR][1000 genomes]
rs13360410	0.90[EUR][1000 genomes]
rs13360536	0.81[EUR][1000 genomes]
rs13362287	0.90[EUR][1000 genomes]
rs1373965	0.90[EUR][1000 genomes]
rs16876417	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs16898989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465130	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28825230	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55792529	0.90[EUR][1000 genomes]
rs56414093	0.89[ASN][1000 genomes]
rs57587453	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681369	0.89[ASN][1000 genomes]
rs58050716	0.90[EUR][1000 genomes]
rs58238009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58652756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59261412	0.82[AFR][1000 genomes]
rs61561045	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452422	0.90[EUR][1000 genomes]
rs6869839	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872195	0.90[EUR][1000 genomes]
rs6872668	0.89[ASN][1000 genomes]
rs6884379	1.00[ASN][1000 genomes]
rs6887061	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887447	0.90[EUR][1000 genomes]
rs6888401	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6893886	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6896772	0.89[ASN][1000 genomes]
rs6897373	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898968	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133677	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133692	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135614	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135635	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73135661	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73137634	0.81[EUR][1000 genomes]
rs73137639	0.81[EUR][1000 genomes]
rs73766239	0.89[ASN][1000 genomes]
rs7707946	0.90[EUR][1000 genomes]
rs7717767	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729317	0.81[EUR][1000 genomes]
rs7736720	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9293277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641	0.89[ASN][1000 genomes]
rs9986216	0.85[AFR][1000 genomes];1.00[ASN][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	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv462222	chr5:80900719-80964452	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv598752	chr5:80900719-80964452	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:80883800-80909200	Weak transcription	HSMM	muscle
3	chr5:80887000-80922400	Weak transcription	Psoas Muscle	Psoas
4	chr5:80887200-80911200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:80893400-80926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:80893600-80909600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:80894400-80905800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:80895200-80909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:80895600-80909200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:80895800-80905800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:80895800-80912000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:80895800-80922600	Weak transcription	Fetal Heart	heart
13	chr5:80897200-80911800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:80897600-80922400	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:80898000-80905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:80898400-80910400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:80899400-80915400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:80900400-80911200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:80903600-80908400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:80903600-80911600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:80904000-80915000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:80904600-80905800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:80904600-80906600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr5:80904800-80906600	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr5:80904800-80906600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:80904800-80906800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:80904800-80906800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr5:80904800-80907200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:80904800-80908000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr5:80904800-80908400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr5:80905000-80905800	Weak transcription	Osteobl	bone
32	chr5:80905000-80906200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:80905000-80906200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:80905000-80921400	Weak transcription	NHDF-Ad	bronchial
35	chr5:80905200-80906000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr5:80905200-80906200	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr5:80905200-80906400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:80905200-80906400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr5:80905200-80906400	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr5:80905200-80906400	ZNF genes & repeats	Fetal Intestine Large	intestine
41	chr5:80905200-80907200	ZNF genes & repeats	GM12878-XiMat	blood
42	chr5:80905200-80926000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:80905400-80905800	ZNF genes & repeats	Fetal Brain Male	brain
44	chr5:80905400-80906000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
45	chr5:80905400-80906000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr5:80905400-80906000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:80905400-80906000	ZNF genes & repeats	Brain Substantia Nigra	brain
48	chr5:80905400-80906000	ZNF genes & repeats	Fetal Brain Female	brain
49	chr5:80905400-80906000	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr5:80905400-80906000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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