Variant report

Variant	rs2838778
Chromosome Location	chr21:46514818-46514819
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	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
2	chr21:46493165..46495720-chr21:46513762..46518212,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12152096	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12185823	0.81[JPT][hapmap]
rs13047803	0.81[JPT][hapmap]
rs1556317	0.81[JPT][hapmap]
rs2003273	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150439	0.81[JPT][hapmap]
rs2838764	0.90[ASW][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs2838767	0.81[MEX][hapmap];1.00[YRI][hapmap]
rs2838787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838797	0.81[JPT][hapmap]
rs2838803	0.81[JPT][hapmap]
rs2838807	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs372766	0.81[JPT][hapmap]
rs377524	0.81[JPT][hapmap]
rs381466	0.85[JPT][hapmap]
rs386762	0.81[JPT][hapmap]
rs422720	0.81[JPT][hapmap]
rs434492	0.81[JPT][hapmap]
rs446158	0.81[JPT][hapmap]
rs7281416	0.81[JPT][hapmap]
rs8128889	0.81[JPT][hapmap]
rs8129315	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130224	0.81[JPT][hapmap]
rs8133307	0.81[JPT][hapmap]
rs8134789	0.81[JPT][hapmap]
rs983749	0.85[JPT][hapmap]
rs9983296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984236	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
3	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:46502000-46515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
7	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr21:46506600-46521400	Weak transcription	NHEK	skin
10	chr21:46507600-46515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr21:46510200-46515600	Weak transcription	K562	blood
13	chr21:46510400-46515200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
15	chr21:46511200-46515200	Enhancers	Primary B cells from cord blood	blood
16	chr21:46511400-46515000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr21:46511800-46515400	Weak transcription	Hela-S3	cervix
18	chr21:46511800-46515600	Weak transcription	HMEC	breast
19	chr21:46511800-46520200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:46512200-46515200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr21:46512200-46515200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr21:46512200-46515800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:46512200-46518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr21:46512600-46515200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr21:46512800-46515000	Enhancers	Fetal Muscle Trunk	muscle
30	chr21:46512800-46516200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr21:46512800-46520400	Enhancers	Fetal Muscle Leg	muscle
32	chr21:46513000-46515000	Enhancers	Primary hematopoietic stem cells	blood
33	chr21:46513000-46515000	Enhancers	Colon Smooth Muscle	Colon
34	chr21:46513000-46515600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr21:46513000-46516600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:46513000-46516600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr21:46513000-46516600	Enhancers	Fetal Heart	heart
38	chr21:46513000-46517600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr21:46513400-46515400	Weak transcription	Gastric	stomach
41	chr21:46513400-46515600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr21:46513400-46518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:46513600-46515800	Weak transcription	Fetal Lung	lung
45	chr21:46513600-46516000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr21:46513600-46516200	Weak transcription	HSMMtube	muscle
47	chr21:46513600-46517200	Weak transcription	Fetal Stomach	stomach
48	chr21:46513600-46517600	Enhancers	Adipose Nuclei	Adipose
49	chr21:46513600-46518600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr21:46513600-46519800	Enhancers	Left Ventricle	heart

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