Variant report

Variant	rs5997912
Chromosome Location	chr22:31593861-31593862
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1034588	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034589	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13054220	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13056485	0.87[ASN][1000 genomes]
rs13158	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858821	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2040533	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2073857	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2078803	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2079431	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2106294	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2228619	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2283879	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413031	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2413032	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2413033	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413034	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413046	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413049	0.90[EUR][1000 genomes]
rs4141404	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4299418	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603880	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820043	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820962	0.85[EUR][1000 genomes]
rs4820963	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749224	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749229	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5753500	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753505	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5753507	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753521	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753543	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997902	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997933	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5997939	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71331284	0.84[ASN][1000 genomes]
rs714909	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715510	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7287267	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737684	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs737887	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737888	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8135344	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8135347	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606830	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9606831	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609254	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609257	0.82[EUR][1000 genomes]
rs9609264	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609265	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609266	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609267	0.85[EUR][1000 genomes]
rs9609268	0.83[EUR][1000 genomes]
rs9621235	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997912	SFI1	cis	Thyroid	GTEx
rs5997912	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr22:31570400-31597800	Weak transcription	HUVEC	blood vessel
6	chr22:31572200-31600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:31574400-31601600	Weak transcription	Fetal Heart	heart
8	chr22:31575800-31602600	Weak transcription	Stomach Mucosa	stomach
9	chr22:31575800-31607600	Weak transcription	Hela-S3	cervix
10	chr22:31576000-31607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr22:31576000-31607800	Weak transcription	A549	lung
12	chr22:31579200-31607400	Weak transcription	K562	blood
13	chr22:31580800-31607600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr22:31581000-31599200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr22:31581400-31607800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:31582400-31602400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr22:31582600-31594000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr22:31582800-31594200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:31582800-31603600	Strong transcription	Liver	Liver
20	chr22:31583000-31598800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:31584000-31608200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:31584800-31595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr22:31584800-31597800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr22:31585600-31599200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr22:31585600-31599800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr22:31585600-31601200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr22:31586000-31603800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr22:31586400-31595200	Weak transcription	HMEC	breast
29	chr22:31587000-31599200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:31587000-31602200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr22:31587600-31596000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr22:31588200-31606600	Strong transcription	Fetal Stomach	stomach
33	chr22:31588400-31594200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr22:31588400-31603400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr22:31588600-31599800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr22:31588600-31606400	Strong transcription	Fetal Intestine Small	intestine
37	chr22:31588800-31594200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr22:31589000-31594000	Strong transcription	HSMMtube	muscle
39	chr22:31589000-31607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr22:31589200-31602200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:31589400-31594200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr22:31589400-31597200	Weak transcription	GM12878-XiMat	blood
43	chr22:31589400-31603600	Strong transcription	Adipose Nuclei	Adipose
44	chr22:31589400-31605800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr22:31589600-31594000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:31590600-31594200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr22:31590600-31596000	Strong transcription	Fetal Thymus	thymus
48	chr22:31590600-31601800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr22:31590600-31602000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr22:31590600-31603200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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