Variant report

Variant	rs3748166
Chromosome Location	chr9:117880149-117880150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1000109	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1000110	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1000111	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10759756	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10759757	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817714	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817715	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817716	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817718	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10982550	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1111784	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11788578	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11792657	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11793679	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12376564	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12378459	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12379019	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12380363	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12554357	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12554651	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1411458	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16936516	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2012566	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2012775	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2900594	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4448357	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4978620	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4979500	0.83[CEU][hapmap]
rs4979501	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57814325	0.88[AFR][1000 genomes]
rs58134557	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58160054	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61508829	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62580502	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6478132	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7018653	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7021057	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7024048	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7025283	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7029844	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7035705	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7039636	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7039915	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7040521	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7849460	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7849467	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7850000	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7850007	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7858535	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7865971	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884790	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117876400-117880200	Enhancers	Hela-S3	cervix
2	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
3	chr9:117877600-117880200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
5	chr9:117878000-117880200	Active TSS	Stomach Smooth Muscle	stomach
6	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
7	chr9:117878200-117880200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:117878200-117880400	Active TSS	Rectal Smooth Muscle	rectum
9	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:117878200-117881000	Active TSS	NHLF	lung
11	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr9:117878400-117880200	Active TSS	Brain Germinal Matrix	brain
15	chr9:117878400-117880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:117878400-117881000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:117878600-117880200	Active TSS	Brain Anterior Caudate	brain
18	chr9:117878600-117880200	Bivalent/Poised TSS	Fetal Brain Male	brain
19	chr9:117878600-117880200	Active TSS	Fetal Muscle Trunk	muscle
20	chr9:117878600-117880400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:117878600-117880600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
22	chr9:117878600-117880600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr9:117878600-117881400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:117878600-117881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:117878800-117880200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:117878800-117880200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr9:117878800-117880800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr9:117879000-117880200	Active TSS	Right Ventricle	heart
29	chr9:117879000-117881400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr9:117879000-117881400	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr9:117879200-117880800	Active TSS	NHDF-Ad	bronchial
32	chr9:117879200-117881000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
33	chr9:117879200-117881000	Active TSS	Esophagus	oesophagus
34	chr9:117879400-117880200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr9:117879400-117880200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:117879400-117880200	Weak transcription	Aorta	Aorta
37	chr9:117879400-117880400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr9:117879400-117880800	Active TSS	NH-A	brain
39	chr9:117879600-117880200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:117879600-117880200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:117879600-117880200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:117879600-117880200	Enhancers	HSMM	muscle
43	chr9:117879600-117880600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:117879600-117881200	Flanking Active TSS	Fetal Lung	lung
45	chr9:117879800-117880200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
46	chr9:117879800-117880200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:117879800-117880200	Enhancers	Lung	lung
48	chr9:117879800-117880200	Active TSS	HMEC	breast
49	chr9:117879800-117880600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:117879800-117880600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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