Variant report

Variant	rs2836999
Chromosome Location	chr21:40761545-40761546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:40761400-40761550	GM12872	blood:	n/a	n/a

No data

(count:22 , 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	chr21:40760349..40761906-chr21:40811512..40813865,2	K562	blood:
15	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
16	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
17	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
18	21:40686083-40686932..21:40757151-40764378	K562	blood:
19	chr21:40761304..40763108-chr21:40765894..40767804,2	MCF-7	breast:
20	chr21:40553901..40555576-chr21:40760955..40763916,2	K562	blood:
21	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
22	chr21:40760208..40762465-chr21:40802596..40804503,2	K562	blood:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1060180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051949	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230	0.87[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	0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs2299739	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2299741	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836994	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.92[CHB][hapmap]
rs2836997	0.82[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837000	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837002	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837003	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837004	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4818035	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[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:30)

SNP	Gene	Cis/trans	Tissue	Source
rs2836999	LCA5L	cis	Thyroid	GTEx
rs2836999	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2836999	LCA5L	cis	Artery Tibial	GTEx
rs2836999	LCA5L	cis	Esophagus Mucosa	GTEx
rs2836999	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2836999	WRB	cis	Esophagus Mucosa	GTEx
rs2836999	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2836999	LOC643790	trans	multi-tissue	Pritchard
rs2836999	WRB	cis	lung	GTEx
rs2836999	WRB	cis	Artery Tibial	GTEx
rs2836999	HMGN1	cis	multi-tissue	Pritchard
rs2836999	LCA5L	cis	lung	GTEx
rs2836999	WRB	cis	parietal	SCAN
rs2836999	WRB	cis	Adipose Subcutaneous	GTEx
rs2836999	LCA5L	cis	Heart Left Ventricle	GTEx
rs2836999	WRB	cis	Esophagus Muscularis	GTEx
rs2836999	WRB	cis	Nerve Tibial	GTEx
rs2836999	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2836999	WRB	cis	multi-tissue	Pritchard
rs2836999	LCA5L	cis	Esophagus Muscularis	GTEx
rs2836999	WRB	cis	cerebellum	SCAN
rs2836999	LCA5L	cis	Nerve Tibial	GTEx
rs2836999	LCA5L	cis	Stomach	GTEx
rs2836999	LCA5L	cis	Whole Blood	GTEx
rs2836999	WRB	cis	Artery Aorta	GTEx
rs2836999	LCA5L	cis	Artery Aorta	GTEx
rs2836999	HMGN1	cis	cerebellum	SCAN
rs2836999	WRB	cis	Thyroid	GTEx
rs2836999	WRB	cis	Whole Blood	GTEx
rs2836999	HMGN1	cis	lymphoblastoid	seeQTL

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	chr21:40760400-40761800	Enhancers	Spleen	Spleen
4	chr21:40760600-40761600	Enhancers	Stomach Mucosa	stomach
5	chr21:40760600-40761800	Enhancers	Liver	Liver
6	chr21:40760600-40761800	Enhancers	Right Ventricle	heart
7	chr21:40760600-40762000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr21:40760600-40762400	Enhancers	Left Ventricle	heart
9	chr21:40760600-40762800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr21:40760600-40763000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:40760600-40763200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:40760600-40763200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr21:40760600-40763600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr21:40760600-40763800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr21:40760600-40763800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr21:40760600-40763800	Weak transcription	Small Intestine	intestine
17	chr21:40760600-40763800	Weak transcription	HSMMtube	muscle
18	chr21:40760600-40763800	Weak transcription	NH-A	brain
19	chr21:40760600-40764000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr21:40760600-40764400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr21:40760600-40771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:40760800-40761800	Enhancers	Fetal Intestine Large	intestine
23	chr21:40760800-40761800	Genic enhancers	Fetal Intestine Small	intestine
24	chr21:40760800-40762200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr21:40760800-40762600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr21:40760800-40762800	Weak transcription	Primary B cells from cord blood	blood
27	chr21:40760800-40763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:40760800-40763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr21:40760800-40763800	Weak transcription	Colon Smooth Muscle	Colon
30	chr21:40760800-40766400	Weak transcription	Fetal Kidney	kidney
31	chr21:40761000-40761600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr21:40761000-40761600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr21:40761000-40761600	Genic enhancers	Brain Germinal Matrix	brain
34	chr21:40761000-40761600	Enhancers	Hela-S3	cervix
35	chr21:40761000-40761800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr21:40761000-40761800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:40761000-40761800	Enhancers	Ovary	ovary
38	chr21:40761000-40761800	Enhancers	Pancreas	Pancrea
39	chr21:40761000-40761800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr21:40761000-40761800	Enhancers	GM12878-XiMat	blood
41	chr21:40761000-40762000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr21:40761000-40762000	Enhancers	Fetal Muscle Leg	muscle
43	chr21:40761000-40762000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr21:40761000-40762000	Weak transcription	NHLF	lung
45	chr21:40761000-40762200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr21:40761000-40762200	Weak transcription	Fetal Brain Female	brain
47	chr21:40761000-40762200	Weak transcription	Fetal Stomach	stomach
48	chr21:40761000-40762200	Enhancers	Stomach Smooth Muscle	stomach
49	chr21:40761000-40762400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr21:40761000-40762400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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