Variant report

Variant	rs2999738
Chromosome Location	chr1:227780879-227780880
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10159323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10916168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1390402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1587156	0.80[AFR][1000 genomes]
rs1817929	1.00[AMR][1000 genomes]
rs1826774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1874372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2313246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2492633	1.00[AMR][1000 genomes]
rs2644142	1.00[AMR][1000 genomes]
rs2814062	1.00[AMR][1000 genomes]
rs2819497	1.00[AMR][1000 genomes]
rs2935148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2935150	0.80[AFR][1000 genomes]
rs2935151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2999739	1.00[AFR][1000 genomes]
rs2999747	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3010184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653513	1.00[AMR][1000 genomes]
rs6426466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6426467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7521659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7540705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs903696	1.00[AMR][1000 genomes]
rs976960	1.00[AMR][1000 genomes]
rs9943170	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227754400-227783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:227760200-227783800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:227760200-227784600	Weak transcription	Fetal Kidney	kidney
4	chr1:227767600-227783400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:227768000-227783600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:227770600-227781200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:227770600-227784400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:227771800-227790600	Weak transcription	Left Ventricle	heart
10	chr1:227773200-227783600	Weak transcription	Psoas Muscle	Psoas
11	chr1:227774600-227783600	Weak transcription	Thymus	Thymus
12	chr1:227774800-227782600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:227774800-227790600	Weak transcription	Gastric	stomach
14	chr1:227774800-227799200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:227777200-227786000	Weak transcription	A549	lung
17	chr1:227777600-227790600	Weak transcription	Ovary	ovary
18	chr1:227778200-227783600	Weak transcription	Pancreas	Pancrea
19	chr1:227778800-227781800	Weak transcription	Primary T cells from cord blood	blood
20	chr1:227778800-227782600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:227779000-227783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:227779200-227799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:227779400-227781000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr1:227779600-227781000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr1:227780000-227781200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:227780000-227781200	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr1:227780000-227783400	Weak transcription	Liver	Liver
28	chr1:227780200-227781200	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr1:227780200-227782600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:227780400-227781000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:227780400-227781000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
32	chr1:227780400-227781000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr1:227780400-227781000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr1:227780400-227781000	ZNF genes & repeats	Fetal Stomach	stomach
35	chr1:227780400-227781200	ZNF genes & repeats	Fetal Brain Female	brain
36	chr1:227780600-227781000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:227780600-227781000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:227780600-227781000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:227780600-227781000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr1:227780600-227781200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:227780600-227781200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr1:227780600-227781200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:227780600-227781200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr1:227780600-227781200	ZNF genes & repeats	Fetal Lung	lung
45	chr1:227780600-227781800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr1:227780800-227782600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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