Variant report

Variant	rs10889259
Chromosome Location	chr1:62341879-62341880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10889260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889264	1.00[AFR][1000 genomes]
rs11207853	1.00[AFR][1000 genomes]
rs17252430	1.00[AMR][1000 genomes]
rs2498986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2498990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2498993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656709	1.00[AMR][1000 genomes]
rs6656711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6687261	1.00[AMR][1000 genomes]
rs6696674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7512340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7522779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7536831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7548755	1.00[AMR][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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
2	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
3	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:62312800-62353200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:62316200-62352200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:62317800-62390400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:62319000-62373800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:62320200-62349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:62320800-62353200	Weak transcription	A549	lung
10	chr1:62321000-62343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:62321600-62353200	Weak transcription	Adipose Nuclei	Adipose
12	chr1:62323800-62355200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:62324400-62361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:62325000-62357400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:62330400-62343600	Weak transcription	Right Ventricle	heart
16	chr1:62330400-62345800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:62330400-62361000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:62330600-62349800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:62330600-62350000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:62331600-62371800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:62331800-62342200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:62331800-62348400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:62331800-62348600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:62331800-62349800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:62331800-62349800	Weak transcription	Primary T cells from cord blood	blood
26	chr1:62331800-62349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:62331800-62352400	Weak transcription	Left Ventricle	heart
28	chr1:62331800-62384200	Weak transcription	Gastric	stomach
29	chr1:62335600-62343600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:62335600-62343600	Weak transcription	Esophagus	oesophagus
31	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
32	chr1:62336200-62362400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:62336400-62352000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:62336400-62360200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:62336600-62380000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:62336800-62356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:62337600-62352800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:62338000-62342000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:62338400-62342200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:62339400-62350400	Weak transcription	Fetal Brain Male	brain
41	chr1:62339600-62350400	Weak transcription	Fetal Kidney	kidney
42	chr1:62339800-62342000	Weak transcription	Fetal Intestine Large	intestine
43	chr1:62339800-62343600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:62339800-62345200	Weak transcription	Aorta	Aorta
45	chr1:62339800-62348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:62339800-62349800	Weak transcription	Ovary	ovary
47	chr1:62339800-62349800	Weak transcription	HepG2	liver
48	chr1:62339800-62353000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:62339800-62353000	Weak transcription	Fetal Stomach	stomach
50	chr1:62339800-62353200	Weak transcription	Psoas Muscle	Psoas

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