Variant report

Variant	rs9809209
Chromosome Location	chr3:51281664-51281665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13080170	0.86[YRI][hapmap]
rs1480360	0.80[YRI][hapmap]
rs2061950	0.82[YRI][hapmap]
rs4619816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4927970	0.92[YRI][hapmap]
rs7649069	0.93[YRI][hapmap]
rs9831735	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9844581	0.93[YRI][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9809209	DOCK3	cis	Thyroid	GTEx
rs9809209	DOCK3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51235800-51285000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:51248000-51282600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:51252000-51288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
5	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
6	chr3:51259800-51284000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:51259800-51284000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:51260000-51284400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:51260000-51284800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:51265800-51284000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:51266400-51284200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:51266400-51284200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:51266400-51284800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:51266400-51297000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:51267000-51297600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:51268000-51296200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:51274800-51284000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:51275400-51284200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:51276400-51284000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:51276600-51284200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:51279600-51282600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:51280400-51284000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:51280400-51286600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:51280400-51298800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:51280600-51284000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:51280800-51285200	Weak transcription	Fetal Brain Female	brain
27	chr3:51281000-51282000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:51281000-51282200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:51281200-51281800	Enhancers	Primary hematopoietic stem cells	blood
30	chr3:51281200-51282400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:51281600-51282400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr3:51281600-51282600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links