Variant report

Variant	rs9978403
Chromosome Location	chr21:45095221-45095222
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	chr21:45092089..45093860-chr21:45094731..45097626,2	K562	blood:
2	chr21:45094040..45098097-chr21:45110651..45114479,4	K562	blood:
3	chr21:45094235..45095825-chr21:45105875..45107390,2	MCF-7	breast:
4	chr21:45093592..45095919-chr21:45110606..45112694,2	MCF-7	breast:
5	chr21:45094660..45096892-chr21:45205328..45207677,2	K562	blood:
6	chr21:45087874..45089696-chr21:45094798..45096349,2	MCF-7	breast:
7	chr21:45078195..45085937-chr21:45087905..45095255,13	K562	blood:
8	chr21:45077374..45079444-chr21:45093929..45096186,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160208	Chromatin interaction
ENSG00000160207	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1041454	0.82[AFR][1000 genomes]
rs1041455	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11911865	1.00[EUR][1000 genomes]
rs12165286	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1378080	0.84[YRI][hapmap]
rs1584918	0.84[YRI][hapmap]
rs2329442	0.87[YRI][hapmap]
rs2329600	1.00[EUR][1000 genomes]
rs2838331	0.91[YRI][hapmap]
rs2838347	1.00[CEU][hapmap]
rs28405975	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4383428	0.85[AFR][1000 genomes]
rs4819270	0.88[YRI][hapmap]
rs61737067	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs718470	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7277539	0.91[YRI][hapmap]
rs73369437	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73908376	1.00[EUR][1000 genomes]
rs8133686	1.00[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs86139	0.88[YRI][hapmap]
rs9306159	0.83[YRI][hapmap]
rs9974343	1.00[CEU][hapmap]
rs9974513	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9974851	0.84[AFR][1000 genomes]
rs9977102	0.86[AFR][1000 genomes]
rs9977212	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9978934	1.00[CEU][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9979935	1.00[CEU][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9980578	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9981291	0.86[YRI][hapmap]
rs9983752	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9984720	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs9984724	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv999311	chr21:45087738-45097588	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1066728	chr21:45089877-45131723	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45080800-45096200	Weak transcription	Psoas Muscle	Psoas
3	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
4	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
5	chr21:45081200-45096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr21:45082000-45101800	Weak transcription	Fetal Kidney	kidney
7	chr21:45082000-45107200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr21:45082400-45097200	Weak transcription	Fetal Brain Male	brain
9	chr21:45082800-45096200	Weak transcription	Colonic Mucosa	Colon
10	chr21:45082800-45116600	Strong transcription	Primary T cells from cord blood	blood
11	chr21:45086000-45117200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:45086400-45095800	Weak transcription	Colon Smooth Muscle	Colon
13	chr21:45086400-45110600	Weak transcription	Stomach Mucosa	stomach
14	chr21:45088400-45117200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr21:45088600-45097400	Strong transcription	K562	blood
16	chr21:45088600-45116400	Strong transcription	Dnd41	blood
17	chr21:45088600-45117000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr21:45088800-45118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr21:45089000-45117000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr21:45089200-45098000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr21:45089200-45098000	Strong transcription	A549	lung
24	chr21:45089200-45098400	Strong transcription	Brain Germinal Matrix	brain
25	chr21:45089200-45099000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:45089200-45099400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:45089200-45101400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:45089200-45115000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr21:45089200-45116000	Strong transcription	Fetal Thymus	thymus
30	chr21:45089200-45116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr21:45089200-45117000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr21:45089200-45117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr21:45089400-45099000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr21:45089400-45116600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr21:45089600-45097800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr21:45089600-45116400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:45089600-45116400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:45089800-45098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr21:45089800-45098000	Strong transcription	NHEK	skin
40	chr21:45089800-45098200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr21:45089800-45098600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr21:45089800-45099200	Strong transcription	Liver	Liver
43	chr21:45089800-45099200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr21:45089800-45100000	Strong transcription	Adipose Nuclei	Adipose
45	chr21:45089800-45107200	Strong transcription	Fetal Muscle Leg	muscle
46	chr21:45089800-45107800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr21:45089800-45108000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr21:45089800-45117000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr21:45089800-45117200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr21:45090000-45107800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links