Variant report

Variant	rs828611
Chromosome Location	chr3:98491184-98491185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1440157	0.92[YRI][hapmap]
rs1818053	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2133575	1.00[AMR][1000 genomes]
rs2173598	0.92[YRI][hapmap]
rs2439230	0.82[AFR][1000 genomes]
rs2439234	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2439235	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs2454683	0.92[YRI][hapmap]
rs2454690	0.83[AFR][1000 genomes]
rs2470856	0.85[YRI][hapmap]
rs2470866	0.80[AFR][1000 genomes]
rs2470868	0.92[YRI][hapmap]
rs2470874	0.81[AFR][1000 genomes]
rs2470884	1.00[AMR][1000 genomes]
rs278375	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs278377	0.91[AFR][1000 genomes]
rs278378	0.92[AFR][1000 genomes]
rs278384	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs278385	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs278386	0.92[AFR][1000 genomes]
rs278389	0.92[AFR][1000 genomes]
rs2922213	0.89[AFR][1000 genomes]
rs5013928	0.92[YRI][hapmap]
rs7630797	0.82[AFR][1000 genomes]
rs828604	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs828606	0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs828607	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs828619	0.86[AFR][1000 genomes]
rs828620	0.89[AFR][1000 genomes]
rs828622	0.88[AFR][1000 genomes]
rs828623	0.89[AFR][1000 genomes]
rs828624	0.89[AFR][1000 genomes]
rs866873	0.88[AFR][1000 genomes]
rs9883226	0.92[YRI][hapmap]
rs996199	0.92[YRI][hapmap];1.00[AMR][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482200-98495800	Weak transcription	Dnd41	blood
3	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
5	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
6	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
8	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
11	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
13	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:98485400-98491600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
24	chr3:98489200-98493200	Strong transcription	HUVEC	blood vessel
25	chr3:98489400-98491200	Strong transcription	HepG2	liver
26	chr3:98489600-98494400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:98489600-98497000	Weak transcription	Lung	lung
28	chr3:98489800-98494000	Weak transcription	Thymus	Thymus
29	chr3:98489800-98494600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:98489800-98494600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:98489800-98495200	Weak transcription	Pancreas	Pancrea
32	chr3:98489800-98495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:98489800-98496000	Weak transcription	Stomach Mucosa	stomach
34	chr3:98489800-98496200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:98489800-98496400	Weak transcription	Placenta	Placenta
36	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
38	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
40	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
42	chr3:98490000-98491200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr3:98490000-98494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:98490000-98495800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:98490000-98496200	Weak transcription	Brain Substantia Nigra	brain
46	chr3:98490000-98496400	Weak transcription	Brain Anterior Caudate	brain
47	chr3:98490200-98494000	Weak transcription	GM12878-XiMat	blood
48	chr3:98490200-98494400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:98490200-98494400	Weak transcription	Fetal Heart	heart
50	chr3:98490200-98496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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