Variant report

Variant	rs2838790
Chromosome Location	chr21:46562024-46562025
allele	C/T
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	chr21:46492190..46501097-chr21:46553481..46562048,38	K562	blood:
2	chr21:46561579..46563104-chr21:46712989..46715797,2	MCF-7	breast:
3	chr21:46560488..46562172-chr21:46702470..46705341,2	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	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:

No data

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2838791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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

No data

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	chr21:46551000-46562400	Weak transcription	HMEC	breast
8	chr21:46551400-46567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr21:46551600-46562400	Weak transcription	Brain Angular Gyrus	brain
10	chr21:46551600-46562600	Genic enhancers	HSMM	muscle
11	chr21:46551800-46565400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr21:46553400-46568600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:46553400-46570600	Weak transcription	Esophagus	oesophagus
14	chr21:46553400-46574600	Weak transcription	Fetal Heart	heart
15	chr21:46553600-46562600	Weak transcription	Placenta	Placenta
16	chr21:46553600-46563000	Weak transcription	Lung	lung
17	chr21:46554800-46564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr21:46555200-46574600	Weak transcription	Right Atrium	heart
19	chr21:46555400-46562400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:46555400-46562400	Weak transcription	Left Ventricle	heart
21	chr21:46555400-46562400	Weak transcription	Right Ventricle	heart
22	chr21:46555600-46571600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr21:46555800-46562600	Weak transcription	Primary T cells from cord blood	blood
24	chr21:46555800-46570800	Weak transcription	Fetal Lung	lung
25	chr21:46555800-46571600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr21:46556200-46562200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr21:46556400-46562800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr21:46556600-46564600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr21:46556600-46581000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr21:46556800-46562800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr21:46557000-46562400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr21:46557000-46571400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
35	chr21:46557400-46562400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr21:46557400-46562800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr21:46557400-46571600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr21:46557400-46577800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr21:46557600-46562400	Weak transcription	Brain Anterior Caudate	brain
40	chr21:46557600-46562600	Weak transcription	Fetal Stomach	stomach
41	chr21:46557600-46573400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr21:46557600-46582600	Weak transcription	Psoas Muscle	Psoas
43	chr21:46558600-46562200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr21:46558600-46562800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:46558600-46571400	Weak transcription	Colon Smooth Muscle	Colon
46	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
47	chr21:46558800-46564400	Weak transcription	NHEK	skin
48	chr21:46558800-46571800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr21:46558800-46571800	Weak transcription	Fetal Intestine Large	intestine
50	chr21:46559200-46565600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links