Variant report

Variant	rs3773725
Chromosome Location	chr3:53207516-53207517
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53196633..53198963-chr3:53206853..53208584,2	K562	blood:
2	chr3:53206286..53208790-chr3:53209926..53212875,3	K562	blood:
3	chr3:53206928..53209011-chr3:53211960..53213627,2	K562	blood:
4	chr3:53189193..53191628-chr3:53207314..53210286,3	MCF-7	breast:
5	chr3:53194470..53197152-chr3:53205968..53208178,2	MCF-7	breast:
6	chr3:53198720..53200683-chr3:53205526..53209327,4	K562	blood:

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11130347	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130350	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872035	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306571	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773727	0.83[ASN][1000 genomes]
rs3773728	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773729	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796256	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821689	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687571	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778964	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
2	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
3	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
5	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:53201200-53210400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:53201400-53212400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:53201400-53212600	Weak transcription	Ovary	ovary
11	chr3:53201400-53212800	Weak transcription	Left Ventricle	heart
12	chr3:53201600-53209400	Weak transcription	HSMM	muscle
13	chr3:53201600-53212800	Weak transcription	NHDF-Ad	bronchial
14	chr3:53201600-53228000	Weak transcription	NH-A	brain
15	chr3:53202000-53207800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:53202000-53209400	Weak transcription	Osteobl	bone
17	chr3:53202000-53212400	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:53202000-53212600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
20	chr3:53202400-53208400	Weak transcription	NHEK	skin
21	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:53203200-53207800	Weak transcription	Right Ventricle	heart
23	chr3:53203200-53226800	Strong transcription	Fetal Stomach	stomach
24	chr3:53203600-53211400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:53203600-53212800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:53203600-53229800	Weak transcription	A549	lung
27	chr3:53203800-53210600	Genic enhancers	Spleen	Spleen
28	chr3:53204000-53210400	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr3:53204000-53212600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:53204200-53211400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:53204600-53213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:53204800-53207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:53205000-53207600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:53205000-53209200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:53205200-53210600	Genic enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:53205400-53208000	Weak transcription	Liver	Liver
37	chr3:53205400-53210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:53205600-53208800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:53205600-53209400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:53205600-53209400	Weak transcription	HMEC	breast
41	chr3:53205600-53210400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:53205600-53211400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
44	chr3:53205800-53209400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:53205800-53213800	Weak transcription	Small Intestine	intestine
46	chr3:53206000-53208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:53206000-53212400	Weak transcription	Fetal Lung	lung
48	chr3:53206000-53212600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:53206000-53213600	Weak transcription	Brain Substantia Nigra	brain
50	chr3:53206000-53213800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links