Variant report

Variant	rs28580454
Chromosome Location	chr7:21528463-21528464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10216269	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10228982	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10233925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10234687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10235230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10238881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10250403	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10250517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10253281	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10254442	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10255890	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10259756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10271650	0.80[AFR][1000 genomes]
rs10274755	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10275955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12674126	1.00[AMR][1000 genomes]
rs2158415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2285941	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28419471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28490171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28528275	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28657649	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661383	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28666837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55840028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55879742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55908918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57142662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57213984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58025439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58223300	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61043546	0.92[AFR][1000 genomes]
rs6946711	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6947378	0.91[AFR][1000 genomes]
rs6953601	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6972886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6973902	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73682608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685128	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685129	0.85[AFR][1000 genomes]
rs73685130	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685131	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685134	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685135	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685138	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73685144	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685152	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685156	0.80[AFR][1000 genomes]
rs7792713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv830921	chr7:21489100-21688016	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21470400-21536400	Weak transcription	Esophagus	oesophagus
2	chr7:21487400-21557000	Weak transcription	Aorta	Aorta
3	chr7:21491000-21536400	Weak transcription	Left Ventricle	heart
4	chr7:21492200-21545200	Weak transcription	Small Intestine	intestine
5	chr7:21493000-21539000	Weak transcription	Spleen	Spleen
6	chr7:21493800-21529600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:21498200-21532400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:21498600-21543600	Weak transcription	Pancreas	Pancrea
9	chr7:21500000-21530400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:21500000-21552800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:21500400-21529800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:21501400-21528800	Weak transcription	Thymus	Thymus
13	chr7:21501400-21531000	Weak transcription	Fetal Intestine Large	intestine
14	chr7:21503200-21532400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:21503200-21532400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:21504000-21532800	Weak transcription	Lung	lung
17	chr7:21505600-21536600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:21506200-21529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:21510200-21530200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:21510800-21531800	Weak transcription	Fetal Intestine Small	intestine
21	chr7:21511600-21531800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:21512800-21529800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:21514000-21536400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:21516200-21556400	Weak transcription	Brain Substantia Nigra	brain
25	chr7:21516400-21530400	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:21517000-21556000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:21517400-21532200	Weak transcription	A549	lung
28	chr7:21518000-21532400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:21518200-21529800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:21518200-21530200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:21518200-21532200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:21518200-21536400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:21518200-21536400	Weak transcription	Fetal Kidney	kidney
34	chr7:21518600-21530000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:21518800-21532000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:21519200-21529800	Weak transcription	Brain Germinal Matrix	brain
37	chr7:21520800-21532000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:21520800-21552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:21521000-21532000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:21521000-21532400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:21521200-21552600	Weak transcription	Brain Angular Gyrus	brain
42	chr7:21521800-21529800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:21522000-21529600	Weak transcription	Fetal Thymus	thymus
44	chr7:21522000-21533800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr7:21522400-21532200	Weak transcription	Adipose Nuclei	Adipose
46	chr7:21522600-21530000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:21522800-21528800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr7:21522800-21529800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:21522800-21529800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr7:21522800-21530000	Weak transcription	H1 Cell Line	embryonic stem cell

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