Variant report

Variant	rs3761819
Chromosome Location	chr9:116276984-116276985
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116276822-116277149	K562	blood:	n/a	n/a
2	POLR2A	chr9:116276284-116277404	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116275302..116278302-chr9:116284369..116288066,3	K562	blood:

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10981793	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10981815	1.00[CHB][hapmap]
rs12338788	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12347382	0.86[ASN][1000 genomes]
rs12351728	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17525042	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553698	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106027	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34142167	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35081798	0.97[EUR][1000 genomes]
rs35120599	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329679	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747813	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3810925	1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810926	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827674	1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276809	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276823	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41306506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41312200	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714377	0.86[ASN][1000 genomes]
rs7042968	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7049221	1.00[CHB][hapmap]
rs72760096	1.00[ASN][1000 genomes]
rs72761906	0.86[ASN][1000 genomes]
rs72761963	0.86[ASN][1000 genomes]
rs72761965	0.86[ASN][1000 genomes]
rs7851937	1.00[CHB][hapmap]
rs7852118	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7854524	1.00[CHB][hapmap]
rs7855434	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7856689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7857217	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7864467	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7864816	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7870142	0.86[ASN][1000 genomes]
rs7870912	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs883025	1.00[CHB][hapmap]
rs884898	1.00[CHB][hapmap]
rs9785299	1.00[CHB][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761819	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116251600-116283800	Weak transcription	Hela-S3	cervix
2	chr9:116264000-116291200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:116264800-116298400	Weak transcription	Brain Germinal Matrix	brain
4	chr9:116266800-116281600	Strong transcription	Fetal Stomach	stomach
5	chr9:116268400-116277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:116268600-116278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:116269000-116288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:116269400-116288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:116269400-116303000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:116269600-116298400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:116270400-116289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:116270400-116290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:116270600-116283800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:116270600-116283800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:116270800-116285200	Weak transcription	Brain Substantia Nigra	brain
16	chr9:116270800-116285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:116271000-116285200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:116271000-116285600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:116271200-116278200	Weak transcription	Adipose Nuclei	Adipose
20	chr9:116271400-116281200	Weak transcription	Fetal Kidney	kidney
21	chr9:116272000-116278200	Weak transcription	Fetal Lung	lung
22	chr9:116273200-116279400	Genic enhancers	Fetal Intestine Small	intestine
23	chr9:116273200-116279600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:116273400-116279400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr9:116273600-116280400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr9:116273600-116280600	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:116273600-116281400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:116273600-116281400	Weak transcription	Right Atrium	heart
29	chr9:116273600-116285400	Weak transcription	Brain Anterior Caudate	brain
30	chr9:116273600-116287000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:116273800-116280400	Strong transcription	HepG2	liver
32	chr9:116274000-116279200	Strong transcription	Left Ventricle	heart
33	chr9:116274000-116281400	Weak transcription	Esophagus	oesophagus
34	chr9:116274200-116277800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:116274400-116279200	Strong transcription	Right Ventricle	heart
36	chr9:116274400-116282400	Weak transcription	Psoas Muscle	Psoas
37	chr9:116274600-116277000	Strong transcription	Fetal Intestine Large	intestine
38	chr9:116274600-116277200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:116274600-116279200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:116274600-116282200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:116274800-116278000	Weak transcription	NHLF	lung
42	chr9:116274800-116278400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:116274800-116279000	Weak transcription	Primary B cells from cord blood	blood
44	chr9:116274800-116279000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:116274800-116279600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:116274800-116280600	Weak transcription	Fetal Heart	heart
47	chr9:116275000-116277200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr9:116275000-116277600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:116275000-116278200	Weak transcription	Osteobl	bone
50	chr9:116275000-116279000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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