Variant report

Variant	rs2299741
Chromosome Location	chr21:40768270-40768271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40750235..40754352-chr21:40768076..40770628,3	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1060180	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.82[EUR][1000 genomes]
rs13051571	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051949	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094874	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244352	0.81[ASN][1000 genomes]
rs2299739	0.83[EUR][1000 genomes]
rs2836994	0.81[ASN][1000 genomes]
rs2836997	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836998	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836999	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837000	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837002	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837003	0.83[ASN][1000 genomes]
rs2837004	0.83[ASN][1000 genomes]
rs2837005	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.88[ASN][1000 genomes]
rs4818035	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2299741	WRB	cis	Nerve Tibial	GTEx
rs2299741	LCA5L	cis	Artery Aorta	GTEx
rs2299741	LCA5L	cis	Esophagus Mucosa	GTEx
rs2299741	LCA5L	cis	Heart Left Ventricle	GTEx
rs2299741	WRB	cis	Whole Blood	GTEx
rs2299741	WRB	cis	lung	GTEx
rs2299741	WRB	cis	Esophagus Muscularis	GTEx
rs2299741	LCA5L	cis	Esophagus Muscularis	GTEx
rs2299741	WRB	cis	Esophagus Mucosa	GTEx
rs2299741	LCA5L	cis	Stomach	GTEx
rs2299741	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2299741	LCA5L	cis	Whole Blood	GTEx
rs2299741	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2299741	WRB	cis	Artery Tibial	GTEx
rs2299741	WRB	cis	Thyroid	GTEx
rs2299741	LCA5L	cis	Artery Tibial	GTEx
rs2299741	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2299741	LCA5L	cis	Thyroid	GTEx
rs2299741	LCA5L	cis	Nerve Tibial	GTEx
rs2299741	WRB	cis	Artery Aorta	GTEx
rs2299741	LCA5L	cis	lung	GTEx
rs2299741	WRB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40760600-40771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40761000-40769800	Weak transcription	HMEC	breast
3	chr21:40761000-40777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:40761000-40779200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr21:40761000-40782600	Weak transcription	Right Atrium	heart
6	chr21:40761200-40771200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:40762200-40768800	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr21:40762200-40770400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr21:40762200-40770400	Strong transcription	Fetal Muscle Leg	muscle
10	chr21:40762200-40770600	Strong transcription	Fetal Brain Female	brain
11	chr21:40762200-40771400	Strong transcription	Fetal Stomach	stomach
12	chr21:40762400-40768400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:40762400-40768800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr21:40762400-40769000	Strong transcription	Primary T cells from cord blood	blood
15	chr21:40762400-40770200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr21:40762400-40770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40762400-40770400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:40762400-40770400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr21:40762400-40770400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr21:40762400-40770400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr21:40762400-40770400	Strong transcription	Ovary	ovary
22	chr21:40762400-40770400	Strong transcription	Thymus	Thymus
23	chr21:40762400-40771000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr21:40762400-40771200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr21:40762600-40768800	Strong transcription	Gastric	stomach
26	chr21:40762600-40769000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr21:40762600-40769000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr21:40762600-40769400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr21:40762600-40770400	Strong transcription	Adipose Nuclei	Adipose
30	chr21:40762600-40770400	Strong transcription	Liver	Liver
31	chr21:40762600-40770400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr21:40762600-40770400	Strong transcription	Fetal Intestine Large	intestine
33	chr21:40762600-40770400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr21:40762600-40770400	Strong transcription	Spleen	Spleen
35	chr21:40762600-40770600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr21:40762600-40770600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr21:40762800-40769400	Strong transcription	Primary B cells from cord blood	blood
38	chr21:40762800-40770000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr21:40762800-40770400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr21:40762800-40770400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:40762800-40770400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr21:40762800-40773000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr21:40763000-40768800	Strong transcription	Fetal Thymus	thymus
44	chr21:40763000-40770400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr21:40763200-40769800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr21:40763200-40769800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr21:40763200-40770200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr21:40763200-40770400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:40763200-40770600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr21:40763400-40768400	Strong transcription	Lung	lung

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