Variant report

Variant	rs2837000
Chromosome Location	chr21:40762255-40762256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:40762160-40762310	GM12873	blood:	n/a	n/a
2	CTCF	chr21:40762240-40762390	GM12871	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
2	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
3	chr21:40760723..40763533-chr21:40790531..40792521,2	MCF-7	breast:
4	chr21:40758499..40762376-chr21:40796781..40799288,3	K562	blood:
5	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
6	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
7	chr21:40759725..40763162-chr21:40764409..40767950,4	K562	blood:
8	chr21:40760590..40763335-chr21:40800736..40802529,2	K562	blood:
9	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
10	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
11	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:
12	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:
13	21:40687235-40690033..21:40757151-40764378	K562	blood:
14	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
15	21:40686083-40686932..21:40757151-40764378	K562	blood:
16	chr21:40761304..40763108-chr21:40765894..40767804,2	MCF-7	breast:
17	chr21:40553901..40555576-chr21:40760955..40763916,2	K562	blood:
18	chr21:40760208..40762465-chr21:40802596..40804503,2	K562	blood:

No data

Variant related genes	Relation type
WRB	TF binding region
ENSG00000182093	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000238556	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 23 )

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

rs_ID	r²[population]
rs1060180	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13051571	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051949	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094874	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244352	0.81[ASN][1000 genomes]
rs2299739	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2299741	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836994	0.81[ASN][1000 genomes]
rs2836997	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836999	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837002	0.91[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	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.88[ASN][1000 genomes]
rs4818035	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2837000	LCA5L	cis	Artery Aorta	GTEx
rs2837000	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837000	LCA5L	cis	Esophagus Muscularis	GTEx
rs2837000	WRB	cis	Thyroid	GTEx
rs2837000	LCA5L	cis	Stomach	GTEx
rs2837000	WRB	cis	Whole Blood	GTEx
rs2837000	LCA5L	cis	Nerve Tibial	GTEx
rs2837000	LCA5L	cis	Heart Left Ventricle	GTEx
rs2837000	WRB	cis	Adipose Subcutaneous	GTEx
rs2837000	WRB	cis	Esophagus Muscularis	GTEx
rs2837000	LCA5L	cis	Thyroid	GTEx
rs2837000	LCA5L	cis	lung	GTEx
rs2837000	WRB	cis	Artery Tibial	GTEx
rs2837000	LCA5L	cis	Whole Blood	GTEx
rs2837000	WRB	cis	lung	GTEx
rs2837000	WRB	cis	Artery Aorta	GTEx
rs2837000	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837000	LCA5L	cis	Esophagus Mucosa	GTEx
rs2837000	LCA5L	cis	Artery Tibial	GTEx
rs2837000	WRB	cis	Esophagus Mucosa	GTEx
rs2837000	WRB	cis	Nerve Tibial	GTEx
rs2837000	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837000	SH3BGR	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40760200-40762400	Weak transcription	Aorta	Aorta
2	chr21:40760200-40763000	Enhancers	Fetal Heart	heart
3	chr21:40760600-40762400	Enhancers	Left Ventricle	heart
4	chr21:40760600-40762800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr21:40760600-40763000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:40760600-40763200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40760600-40763200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:40760600-40763600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr21:40760600-40763800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr21:40760600-40763800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:40760600-40763800	Weak transcription	Small Intestine	intestine
12	chr21:40760600-40763800	Weak transcription	HSMMtube	muscle
13	chr21:40760600-40763800	Weak transcription	NH-A	brain
14	chr21:40760600-40764000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr21:40760600-40764400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr21:40760600-40771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40760800-40762600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:40760800-40762800	Weak transcription	Primary B cells from cord blood	blood
19	chr21:40760800-40763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr21:40760800-40763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr21:40760800-40763800	Weak transcription	Colon Smooth Muscle	Colon
22	chr21:40760800-40766400	Weak transcription	Fetal Kidney	kidney
23	chr21:40761000-40762400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:40761000-40762400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:40761000-40762400	Weak transcription	Primary T cells from cord blood	blood
26	chr21:40761000-40762400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:40761000-40762400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:40761000-40762400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr21:40761000-40762400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr21:40761000-40762400	Enhancers	Fetal Muscle Trunk	muscle
31	chr21:40761000-40762400	Weak transcription	Thymus	Thymus
32	chr21:40761000-40762400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr21:40761000-40762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:40761000-40762600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr21:40761000-40762600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr21:40761000-40762600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr21:40761000-40762600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr21:40761000-40762600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr21:40761000-40762600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr21:40761000-40762600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:40761000-40762600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr21:40761000-40762600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr21:40761000-40762600	Weak transcription	Brain Angular Gyrus	brain
44	chr21:40761000-40762600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr21:40761000-40762600	Weak transcription	Brain Substantia Nigra	brain
46	chr21:40761000-40762600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr21:40761000-40762600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr21:40761000-40762600	Enhancers	K562	blood
49	chr21:40761000-40762600	Weak transcription	Osteobl	bone
50	chr21:40761000-40762800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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