Variant report

Variant	rs1407828
Chromosome Location	chr13:49652518-49652519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2025315	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3012131	1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3012137	1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs61158798	1.00[AFR][1000 genomes]
rs7992530	1.00[YRI][hapmap]
rs9568165	1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr13:49601800-49660600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:49608800-49658800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr13:49627200-49656800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:49627400-49656800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:49627400-49672400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:49628600-49656600	Weak transcription	Thymus	Thymus
8	chr13:49628800-49657000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:49629000-49665600	Weak transcription	Lung	lung
10	chr13:49629600-49665400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:49630200-49656800	Weak transcription	Aorta	Aorta
12	chr13:49630400-49664000	Weak transcription	Fetal Intestine Small	intestine
13	chr13:49632200-49664800	Weak transcription	Fetal Lung	lung
14	chr13:49635000-49664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:49636200-49652800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:49636800-49652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:49636800-49667800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:49637800-49656200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:49638800-49656400	Weak transcription	HMEC	breast
20	chr13:49639000-49656400	Weak transcription	NHEK	skin
21	chr13:49639600-49656800	Weak transcription	Gastric	stomach
22	chr13:49639600-49656800	Weak transcription	Ovary	ovary
23	chr13:49639600-49687200	Weak transcription	Pancreas	Pancrea
24	chr13:49640600-49683800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:49641200-49663200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr13:49641800-49671600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:49642800-49654400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:49643800-49657000	Weak transcription	HSMM	muscle
29	chr13:49645000-49671000	Weak transcription	Small Intestine	intestine
30	chr13:49646400-49660800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:49647600-49656200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr13:49648600-49656600	Weak transcription	HSMMtube	muscle
33	chr13:49648800-49659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr13:49649000-49658600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:49649200-49653000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr13:49649200-49655400	Strong transcription	Placenta	Placenta
37	chr13:49649400-49684200	Weak transcription	Right Ventricle	heart
38	chr13:49649600-49653800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr13:49649600-49654000	Weak transcription	HepG2	liver
40	chr13:49649600-49656400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr13:49649600-49656800	Weak transcription	NHLF	lung
42	chr13:49649600-49660400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:49649800-49657000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr13:49649800-49657000	Weak transcription	K562	blood
45	chr13:49649800-49671600	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:49650000-49652800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr13:49650000-49653000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr13:49650200-49658000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:49650400-49658600	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:49650800-49656600	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links