Variant report

Variant	rs3773731
Chromosome Location	chr3:53202143-53202144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53201349..53203346-chr3:53232423..53233942,2	MCF-7	breast:
2	chr3:53199183..53202732-chr3:53204136..53207026,5	K562	blood:
3	chr3:53187180..53188996-chr3:53201461..53203249,2	MCF-7	breast:
4	chr3:53201393..53204034-chr3:53289191..53291419,2	MCF-7	breast:
5	chr3:53199690..53202730-chr3:53210054..53211867,3	MCF-7	breast:
6	chr3:53150999..53152695-chr3:53199764..53202403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11924565	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1483185	0.88[ASN][1000 genomes]
rs1483186	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1483187	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2242305	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3773724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3773726	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3773727	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3773733	0.88[ASN][1000 genomes]
rs57046386	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62254282	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6775022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797662	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72537447	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630325	0.92[AMR][1000 genomes];0.88[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:119 , 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	chr3:53196600-53204000	Weak transcription	Small Intestine	intestine
4	chr3:53197200-53205400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:53197400-53202200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:53197400-53203000	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr3:53197400-53207000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:53197600-53204200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:53197600-53206600	Genic enhancers	Fetal Intestine Small	intestine
11	chr3:53197600-53206800	Weak transcription	Primary T cells from cord blood	blood
12	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
13	chr3:53197800-53202800	Enhancers	Brain Anterior Caudate	brain
14	chr3:53197800-53203800	Weak transcription	Thymus	Thymus
15	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:53198000-53206800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:53198600-53202200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:53198800-53202200	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:53199200-53202600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:53199600-53202400	Enhancers	Brain Hippocampus Middle	brain
22	chr3:53199600-53202400	Strong transcription	NHEK	skin
23	chr3:53199600-53203000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:53199600-53205000	Genic enhancers	Esophagus	oesophagus
25	chr3:53199800-53202400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:53199800-53203200	Enhancers	Placenta	Placenta
27	chr3:53200000-53202400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:53200200-53202800	Genic enhancers	Fetal Stomach	stomach
29	chr3:53200200-53204000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:53200200-53205800	Enhancers	Fetal Muscle Leg	muscle
31	chr3:53200200-53206400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:53200200-53207200	Enhancers	Fetal Thymus	thymus
33	chr3:53200400-53202600	Enhancers	Liver	Liver
34	chr3:53200400-53202800	Enhancers	HSMMtube	muscle
35	chr3:53200400-53205000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:53200400-53206200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:53200600-53202600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:53200600-53202600	Enhancers	Fetal Lung	lung
39	chr3:53200600-53204800	Weak transcription	Fetal Brain Male	brain
40	chr3:53200600-53206200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:53200600-53206200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:53200600-53206400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:53200600-53206800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:53200800-53202400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:53200800-53203600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr3:53200800-53203600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:53200800-53204000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:53200800-53204600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr3:53200800-53204600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links