Variant report

Variant	rs3789876
Chromosome Location	chr9:117785423-117785424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117158967..117160760-chr9:117784217..117787013,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10118726	1.00[CEU][hapmap]
rs12683163	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16932058	0.84[AMR][1000 genomes]
rs16932066	1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[AMR][1000 genomes]
rs16932085	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2274753	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2274754	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34166409	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3748172	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs57060600	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60347203	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117773600-117787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:117776400-117786000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:117776800-117791600	Weak transcription	Fetal Lung	lung
5	chr9:117779800-117787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:117781000-117788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:117781800-117791600	Weak transcription	Aorta	Aorta
8	chr9:117781800-117797400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:117781800-117798200	Weak transcription	Fetal Intestine Large	intestine
10	chr9:117781800-117798400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:117782000-117788200	Weak transcription	Spleen	Spleen
13	chr9:117782000-117789600	Weak transcription	Gastric	stomach
14	chr9:117782200-117786000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:117782200-117786600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
17	chr9:117783000-117787200	Strong transcription	Colon Smooth Muscle	Colon
18	chr9:117783000-117787400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:117783200-117785600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:117783200-117785600	Strong transcription	NHEK	skin
21	chr9:117783200-117786800	Strong transcription	Fetal Muscle Leg	muscle
22	chr9:117783200-117789000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:117783200-117790000	Strong transcription	Fetal Stomach	stomach
24	chr9:117783200-117792400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:117783200-117796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:117783800-117785600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:117784200-117786800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr9:117784200-117787400	Genic enhancers	NHDF-Ad	bronchial
29	chr9:117784400-117786600	Genic enhancers	NHLF	lung
30	chr9:117784400-117788200	Genic enhancers	Osteobl	bone
31	chr9:117784400-117789000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:117784400-117790200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr9:117784400-117791600	Weak transcription	Fetal Kidney	kidney
34	chr9:117784600-117786200	Enhancers	HSMM	muscle
35	chr9:117784600-117788000	Genic enhancers	NH-A	brain
36	chr9:117784600-117788200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117784600-117788400	Enhancers	HMEC	breast
38	chr9:117784800-117786000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:117784800-117786600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:117785000-117786200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:117785000-117786800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:117785200-117786400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:117785200-117787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:117785400-117785800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:117785400-117786000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:117785400-117786000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:117785400-117786400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:117785400-117787000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:117785400-117787200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links