Variant report

Variant	rs2838791
Chromosome Location	chr21:46563014-46563015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46492650..46496379-chr21:46562233..46566243,5	K562	blood:
2	chr21:46556578..46559478-chr21:46562183..46565396,3	MCF-7	breast:
3	chr21:46561579..46563104-chr21:46712989..46715797,2	MCF-7	breast:
4	chr21:46558032..46564399-chr21:46706240..46711834,9	MCF-7	breast:
5	chr21:46560497..46564169-chr21:46565170..46570508,5	K562	blood:
6	chr21:46493357..46495279-chr21:46560970..46563462,2	MCF-7	breast:
7	chr21:46561382..46564170-chr21:46683644..46686214,2	MCF-7	breast:
8	chr21:46562323..46564274-chr21:46565589..46568586,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000215447	Chromatin interaction
ENSG00000186866	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000223768	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11088982	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11088983	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs12185823	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs13047803	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1537121	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1556317	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2150439	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2838790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838797	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2838803	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2838807	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs372766	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs377524	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs381466	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs386762	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs422720	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs427943	0.81[CEU][hapmap]
rs434492	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs446158	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4819030	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs4819031	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs7281416	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7281757	0.82[JPT][hapmap]
rs8128889	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8130224	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8133307	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs8134789	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs983749	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]

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	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	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
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838791	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46532600-46570600	Weak transcription	Dnd41	blood
2	chr21:46548600-46571600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr21:46549800-46567600	Weak transcription	Gastric	stomach
4	chr21:46550000-46567800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr21:46550400-46571200	Weak transcription	Brain Germinal Matrix	brain
6	chr21:46550800-46563600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr21:46551400-46567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:46551800-46565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:46553400-46568600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr21:46553400-46570600	Weak transcription	Esophagus	oesophagus
11	chr21:46553400-46574600	Weak transcription	Fetal Heart	heart
12	chr21:46554800-46564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr21:46555200-46574600	Weak transcription	Right Atrium	heart
14	chr21:46555600-46571600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr21:46555800-46570800	Weak transcription	Fetal Lung	lung
16	chr21:46555800-46571600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr21:46556600-46564600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr21:46556600-46581000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr21:46557000-46571400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
22	chr21:46557400-46571600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:46557400-46577800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr21:46557600-46573400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr21:46557600-46582600	Weak transcription	Psoas Muscle	Psoas
26	chr21:46558600-46571400	Weak transcription	Colon Smooth Muscle	Colon
27	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
28	chr21:46558800-46564400	Weak transcription	NHEK	skin
29	chr21:46558800-46571800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:46558800-46571800	Weak transcription	Fetal Intestine Large	intestine
31	chr21:46559200-46565600	Weak transcription	Primary B cells from cord blood	blood
32	chr21:46559600-46567200	Weak transcription	K562	blood
33	chr21:46560600-46565000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr21:46560800-46563200	Weak transcription	Fetal Intestine Small	intestine
35	chr21:46560800-46578600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr21:46560800-46586400	Weak transcription	Liver	Liver
37	chr21:46561000-46563400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr21:46561200-46571600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr21:46561400-46571600	Weak transcription	Thymus	Thymus
40	chr21:46561400-46576000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:46561600-46563200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr21:46561600-46563200	Enhancers	NHDF-Ad	bronchial
43	chr21:46561600-46563400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr21:46561600-46563800	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr21:46561800-46563200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr21:46561800-46563200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:46561800-46563600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr21:46562000-46563200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:46562000-46563200	Enhancers	Osteobl	bone
50	chr21:46562000-46567400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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