Variant report

Variant	rs72978398
Chromosome Location	chr3:133658648-133658649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133655319..133659400-chr3:133660671..133664345,4	MCF-7	breast:
2	chr3:133656338..133659550-chr3:133661023..133664144,3	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs59416045	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59935979	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72978388	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72980303	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980304	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980310	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980320	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980324	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980326	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72980351	0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133647000-133661800	Weak transcription	Gastric	stomach
2	chr3:133647400-133661000	Weak transcription	Fetal Thymus	thymus
3	chr3:133647800-133661000	Weak transcription	Lung	lung
4	chr3:133650200-133662600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:133651800-133663400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:133654000-133662600	Weak transcription	Fetal Intestine Large	intestine
7	chr3:133654200-133659200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:133654400-133661800	Weak transcription	Colonic Mucosa	Colon
9	chr3:133654400-133662200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:133654400-133662600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:133654400-133662600	Weak transcription	Small Intestine	intestine
12	chr3:133654600-133662600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:133654800-133661400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:133655000-133661400	Weak transcription	Stomach Mucosa	stomach
15	chr3:133655400-133658800	Enhancers	Fetal Muscle Leg	muscle
16	chr3:133655400-133660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:133655600-133662600	Weak transcription	Fetal Kidney	kidney
18	chr3:133656000-133661000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:133656200-133659800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:133656200-133660600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:133656600-133660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:133656800-133660200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:133656800-133660400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:133656800-133662600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:133657000-133661000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:133657000-133661800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:133657000-133662200	Weak transcription	NHDF-Ad	bronchial
28	chr3:133657000-133662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:133657200-133661400	Weak transcription	Fetal Stomach	stomach
30	chr3:133657400-133661200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:133657400-133662600	Weak transcription	Left Ventricle	heart
32	chr3:133657400-133663000	Weak transcription	Aorta	Aorta
33	chr3:133657800-133659000	Weak transcription	Spleen	Spleen
34	chr3:133658200-133659600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:133658200-133659800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:133658400-133661800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:133658600-133660200	Weak transcription	Right Atrium	heart
38	chr3:133658600-133660400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:133658600-133662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links