Variant report

Variant	rs9825944
Chromosome Location	chr3:49996505-49996506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12330297	1.00[AFR][1000 genomes]
rs13316958	0.87[AFR][1000 genomes]
rs13318943	1.00[AFR][1000 genomes]
rs13323932	0.87[AFR][1000 genomes]
rs13324545	1.00[AFR][1000 genomes]
rs55968312	1.00[AFR][1000 genomes]
rs9811223	0.87[AFR][1000 genomes]
rs9819888	1.00[AFR][1000 genomes]
rs9828683	1.00[AFR][1000 genomes]
rs9835029	1.00[AFR][1000 genomes]
rs9835838	0.87[AFR][1000 genomes]
rs9847587	0.86[AFR][1000 genomes]
rs9849605	1.00[AFR][1000 genomes]
rs9850145	0.87[AFR][1000 genomes]
rs9852055	0.86[AFR][1000 genomes]
rs9862830	1.00[AFR][1000 genomes]
rs9863339	1.00[AFR][1000 genomes]
rs9864231	1.00[AFR][1000 genomes]
rs9866016	1.00[AFR][1000 genomes]
rs9875038	1.00[AFR][1000 genomes]
rs9883977	0.87[AFR][1000 genomes]

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	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:49978800-50004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
5	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:49979000-49997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:49979000-50000000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:49979000-50000600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:49979000-50001000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:49979000-50003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:49979000-50003600	Weak transcription	Right Ventricle	heart
12	chr3:49979000-50005200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:49979000-50010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:49979400-49999000	Weak transcription	Fetal Thymus	thymus
15	chr3:49979400-49999600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:49979400-50000400	Weak transcription	Brain Germinal Matrix	brain
17	chr3:49979600-49999800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:49979600-50004200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:49980400-49997400	Weak transcription	HepG2	liver
20	chr3:49980400-50003600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:49980600-49999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:49980600-50000000	Weak transcription	Dnd41	blood
23	chr3:49980600-50001800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:49981400-49999800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:49981600-49999600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:49983800-49997600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49983800-49999200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:49983800-50003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:49984000-49998200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:49984000-50000400	Weak transcription	Fetal Intestine Large	intestine
31	chr3:49984200-49998400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:49985600-50000600	Weak transcription	Primary B cells from cord blood	blood
33	chr3:49986000-50000600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:49987000-49997400	Weak transcription	Right Atrium	heart
35	chr3:49987600-49997800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:49987800-49997400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:49988000-49997200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:49988000-49997400	Weak transcription	Left Ventricle	heart
39	chr3:49988000-50000600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:49988000-50003000	Weak transcription	NHEK	skin
41	chr3:49988000-50003600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:49988000-50004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:49988200-49997200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:49988200-49997400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:49988200-49997400	Weak transcription	Ovary	ovary
46	chr3:49988200-50007000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:49988200-50007400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:49988200-50010200	Weak transcription	Gastric	stomach
49	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:49988400-49998800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links