Variant report

Variant	rs62256050
Chromosome Location	chr3:53308159-53308160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53302801..53305570-chr3:53307574..53309854,2	MCF-7	breast:
2	chr3:53288591..53290620-chr3:53306397..53309238,2	K562	blood:
3	chr3:53288591..53290442-chr3:53307738..53310063,2	K562	blood:
4	chr3:53303046..53306118-chr3:53306275..53309308,4	K562	blood:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10433617	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10433618	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1108506	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11551405	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17030933	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17030934	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17234771	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17235667	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41275543	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56654807	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58558806	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59145995	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255989	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62255993	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62255994	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62255999	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62256000	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62256003	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256009	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256043	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62256049	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256053	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256962	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256964	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256965	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256966	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256968	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256969	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62257004	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62257007	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257009	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62257011	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62257013	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257024	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6780100	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6805246	0.82[AMR][1000 genomes]
rs73080266	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73080271	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73080273	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73080295	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73082274	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7622159	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9830594	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9830895	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9846315	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9850440	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9864057	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53300600-53312800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:53304200-53316600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:53304400-53316600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:53304400-53318000	Weak transcription	Fetal Intestine Large	intestine
5	chr3:53304600-53309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:53304600-53309000	Weak transcription	Pancreas	Pancrea
7	chr3:53304600-53315200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:53304600-53315400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:53304600-53315600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:53304600-53316600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:53304600-53316600	Weak transcription	Liver	Liver
12	chr3:53304600-53316600	Weak transcription	Lung	lung
13	chr3:53304600-53316600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:53304600-53316800	Weak transcription	Ovary	ovary
15	chr3:53304600-53317800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:53304600-53317800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:53304600-53318000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:53304600-53318600	Weak transcription	Gastric	stomach
19	chr3:53304600-53320600	Weak transcription	Brain Angular Gyrus	brain
20	chr3:53304600-53325600	Weak transcription	Fetal Heart	heart
21	chr3:53304600-53326200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:53304800-53308400	Weak transcription	Fetal Lung	lung
23	chr3:53304800-53309000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:53304800-53309200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:53304800-53309200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:53304800-53309200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:53304800-53309400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:53304800-53316600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:53304800-53316600	Weak transcription	Aorta	Aorta
30	chr3:53304800-53316600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:53304800-53316800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:53304800-53318400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:53304800-53319000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:53304800-53319400	Weak transcription	HSMM	muscle
35	chr3:53305000-53309000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:53305000-53309000	Weak transcription	Dnd41	blood
37	chr3:53305000-53309200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:53305000-53309400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:53305000-53312600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:53305000-53315200	Weak transcription	Primary B cells from cord blood	blood
41	chr3:53305000-53315200	Weak transcription	Adipose Nuclei	Adipose
42	chr3:53305000-53316600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:53305000-53316600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:53305000-53316600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:53305000-53316600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:53305000-53316600	Weak transcription	GM12878-XiMat	blood
47	chr3:53305000-53316600	Weak transcription	HSMMtube	muscle
48	chr3:53305000-53316600	Weak transcription	HUVEC	blood vessel
49	chr3:53305000-53316800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:53305000-53316800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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