Variant report

Variant	rs1888987
Chromosome Location	chr1:62374897-62374898
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1332637	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2016237	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2095092	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2151122	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2245512	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2482850	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482851	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482854	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2482856	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2482897	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2482899	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2499002	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2499003	0.89[EUR][1000 genomes]
rs2499004	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2499005	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6699016	0.86[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	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
2	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
3	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
4	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
5	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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
2	chr1:62317800-62390400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:62331800-62384200	Weak transcription	Gastric	stomach
4	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
5	chr1:62336600-62380000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:62340400-62399200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:62346000-62389400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:62350200-62397600	Weak transcription	Esophagus	oesophagus
10	chr1:62350600-62380200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:62350600-62391600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:62350800-62395800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:62350800-62397800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:62350800-62417600	Weak transcription	Ovary	ovary
16	chr1:62352200-62375200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:62353400-62378400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:62353400-62380200	Weak transcription	Aorta	Aorta
19	chr1:62353600-62396000	Weak transcription	Fetal Kidney	kidney
20	chr1:62353800-62385400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:62354200-62375200	Weak transcription	Left Ventricle	heart
23	chr1:62361200-62390800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:62361600-62375200	Weak transcription	Lung	lung
25	chr1:62361600-62382800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:62361600-62391800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:62361800-62376200	Weak transcription	Fetal Stomach	stomach
29	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:62363000-62391800	Weak transcription	Stomach Mucosa	stomach
31	chr1:62363400-62391400	Weak transcription	A549	lung
32	chr1:62363800-62377000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:62364600-62380200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:62366000-62375000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:62366200-62379000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:62367000-62378600	Weak transcription	HepG2	liver
37	chr1:62367600-62380200	Weak transcription	Liver	Liver
38	chr1:62368000-62375000	Weak transcription	Fetal Intestine Large	intestine
39	chr1:62369000-62375800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:62369000-62376400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:62370000-62379800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:62370400-62376800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:62371200-62376800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:62372200-62379000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:62372400-62382200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:62372600-62380400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:62372600-62384200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:62372600-62385000	Weak transcription	H1 Cell Line	embryonic stem cell

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