Variant report

Variant	rs72990577
Chromosome Location	chr3:138499616-138499617
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138497768..138501036-chr3:138504474..138507070,3	MCF-7	breast:
2	chr3:138497639..138499838-chr3:138521505..138523466,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12107289	1.00[AMR][1000 genomes]
rs12108068	1.00[AMR][1000 genomes]
rs28473201	1.00[AMR][1000 genomes]
rs3729699	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56382670	0.95[AFR][1000 genomes]
rs56927625	0.84[AFR][1000 genomes]
rs57216562	1.00[AMR][1000 genomes]
rs58671569	1.00[AMR][1000 genomes]
rs59797415	1.00[AMR][1000 genomes]
rs59813438	1.00[AMR][1000 genomes]
rs60295689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60850836	1.00[AMR][1000 genomes]
rs60987624	0.84[AFR][1000 genomes]
rs6795773	1.00[AMR][1000 genomes]
rs72972909	0.95[AFR][1000 genomes]
rs72972913	0.93[AFR][1000 genomes]
rs72972920	0.87[AFR][1000 genomes]
rs72988878	1.00[AMR][1000 genomes]
rs72990507	1.00[AMR][1000 genomes]
rs72990541	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990552	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73866224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv967071	chr3:138496873-138501049	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
2	chr3:138488000-138499800	Weak transcription	Thymus	Thymus
3	chr3:138488000-138504600	Weak transcription	Primary B cells from cord blood	blood
4	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
5	chr3:138488200-138503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:138488400-138512200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:138489000-138511600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:138489200-138500000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:138489200-138519200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:138492400-138515800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:138494200-138505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:138494400-138500200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:138494400-138511600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:138494400-138511600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:138494600-138499800	Weak transcription	Colonic Mucosa	Colon
16	chr3:138494600-138499800	Weak transcription	Stomach Mucosa	stomach
17	chr3:138494600-138504400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:138494600-138510200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:138494600-138510200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:138494600-138510200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:138494600-138511000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:138494600-138512200	Weak transcription	Esophagus	oesophagus
23	chr3:138494600-138513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:138494600-138513600	Weak transcription	HSMM	muscle
25	chr3:138494600-138515800	Weak transcription	Ovary	ovary
26	chr3:138494600-138518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:138494600-138521200	Weak transcription	Right Ventricle	heart
28	chr3:138494800-138501200	Weak transcription	Fetal Heart	heart
29	chr3:138494800-138510200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:138494800-138537000	Weak transcription	HUVEC	blood vessel
31	chr3:138495400-138505000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:138495400-138506200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:138495600-138505200	Weak transcription	Osteobl	bone
34	chr3:138495600-138505400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:138495600-138505600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:138495600-138505600	Weak transcription	Adipose Nuclei	Adipose
37	chr3:138495600-138505600	Weak transcription	HMEC	breast
38	chr3:138495600-138517600	Weak transcription	HSMMtube	muscle
39	chr3:138495800-138505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:138496000-138505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:138496200-138499800	Weak transcription	Placenta	Placenta
42	chr3:138496200-138505600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:138496200-138506800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:138496200-138513600	Weak transcription	NHLF	lung
45	chr3:138496200-138516200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:138496200-138521400	Weak transcription	Brain Anterior Caudate	brain
47	chr3:138496200-138522400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:138496400-138500000	Weak transcription	Hela-S3	cervix
49	chr3:138496400-138505200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:138496400-138505200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links