Variant report

Variant	rs9983435
Chromosome Location	chr21:40816631-40816632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11575944	0.95[ASN][1000 genomes]
rs12483547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050837	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051054	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051142	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2009713	0.85[TSI][hapmap]
rs2049823	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837010	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837011	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2837012	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837013	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837014	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2837016	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2837027	0.88[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837028	0.83[ASN][1000 genomes]
rs2837033	0.86[ASN][1000 genomes]
rs2837038	0.88[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4816626	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816628	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276842	0.85[ASN][1000 genomes]
rs7277602	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277633	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130381	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9979289	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979353	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9983100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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	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
3	esv20340	chr21:40814284-40816976	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs9983435	C21orf121	cis	cerebellum	SCAN
rs9983435	LCA5L	cis	parietal	SCAN
rs9983435	HMGN1	cis	lymphoblastoid	seeQTL
rs9983435	LCA5L	cis	Esophagus Mucosa	GTEx
rs9983435	WRB	cis	lung	GTEx
rs9983435	WRB	cis	cerebellum	SCAN
rs9983435	LCA5L	cis	Adipose Subcutaneous	GTEx
rs9983435	WRB	cis	multi-tissue	Pritchard
rs9983435	SH3BGR	cis	Thyroid	GTEx
rs9983435	LCA5L	cis	Esophagus Muscularis	GTEx
rs9983435	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs9983435	LCA5L	cis	Artery Tibial	GTEx
rs9983435	LCA5L	cis	Artery Aorta	GTEx
rs9983435	WRB	cis	Thyroid	GTEx
rs9983435	LCA5L	cis	Muscle Skeletal	GTEx
rs9983435	LCA5L	cis	Thyroid	GTEx
rs9983435	WRB	cis	Artery Tibial	GTEx
rs9983435	LCA5L	cis	Stomach	GTEx
rs9983435	LCA5L	cis	Nerve Tibial	GTEx
rs9983435	LCA5L	cis	lung	GTEx
rs9983435	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs9983435	WRB	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40814600-40816800	Weak transcription	Ovary	ovary
2	chr21:40815800-40816800	Enhancers	Fetal Thymus	thymus
3	chr21:40816200-40816800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr21:40816400-40816800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:40816400-40816800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:40816400-40816800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr21:40816400-40816800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:40816400-40816800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr21:40816400-40816800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr21:40816400-40816800	Enhancers	Liver	Liver
11	chr21:40816400-40816800	Flanking Active TSS	HSMMtube	muscle
12	chr21:40816400-40817000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr21:40816400-40817000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:40816400-40817000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr21:40816400-40817000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:40816400-40817000	Flanking Active TSS	Fetal Brain Female	brain
17	chr21:40816400-40817000	Enhancers	Placenta	Placenta
18	chr21:40816400-40817000	Flanking Active TSS	Osteobl	bone
19	chr21:40816400-40817200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:40816400-40817200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:40816400-40817200	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr21:40816400-40817200	Enhancers	Spleen	Spleen
23	chr21:40816400-40818200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr21:40816400-40818200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr21:40816600-40816800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr21:40816600-40816800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
27	chr21:40816600-40816800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr21:40816600-40816800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
29	chr21:40816600-40816800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr21:40816600-40816800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr21:40816600-40816800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr21:40816600-40816800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:40816600-40816800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr21:40816600-40816800	Enhancers	Brain Substantia Nigra	brain
35	chr21:40816600-40816800	Flanking Active TSS	Fetal Heart	heart
36	chr21:40816600-40816800	Enhancers	Left Ventricle	heart
37	chr21:40816600-40816800	Enhancers	Pancreas	Pancrea
38	chr21:40816600-40816800	Enhancers	Psoas Muscle	Psoas
39	chr21:40816600-40816800	Flanking Active TSS	Right Atrium	heart
40	chr21:40816600-40816800	Enhancers	Stomach Mucosa	stomach
41	chr21:40816600-40816800	Enhancers	Thymus	Thymus
42	chr21:40816600-40816800	Flanking Active TSS	A549	lung
43	chr21:40816600-40816800	Flanking Active TSS	HSMM	muscle
44	chr21:40816600-40816800	Flanking Active TSS	NHDF-Ad	bronchial
45	chr21:40816600-40817000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr21:40816600-40817000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr21:40816600-40817000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr21:40816600-40817000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr21:40816600-40817000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr21:40816600-40817000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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