Variant report

Variant	rs2909207
Chromosome Location	chr17:66439605-66439606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66438851..66440456-chr17:66442013..66443633,2	K562	blood:
2	chr17:66435227..66440274-chr17:66440311..66442952,5	MCF-7	breast:
3	chr17:66437986..66439802-chr17:66451933..66454394,2	MCF-7	breast:
4	chr17:66437281..66439635-chr17:66443689..66446855,5	K562	blood:

Variant related genes	Relation type
ENSG00000070540	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11077558	0.86[CHB][hapmap]
rs1112737	0.91[CHB][hapmap]
rs1808335	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2909209	0.94[EUR][1000 genomes]
rs2909213	0.89[CEU][hapmap]
rs2909218	0.81[GIH][hapmap]
rs2952279	0.82[TSI][hapmap]
rs2952289	0.81[GIH][hapmap]
rs2952294	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs2952295	0.92[EUR][1000 genomes]
rs2952296	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6501468	0.94[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6501477	0.88[JPT][hapmap]
rs8072338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883541	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2909207	CD79B	cis	cerebellum	SCAN
rs2909207	TANC2	cis	cerebellum	SCAN
rs2909207	SDC1	trans	lymphoblastoid	seeQTL
rs2909207	PRKAR1A	cis	multi-tissue	Pritchard
rs2909207	STRADA	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:66420800-66446400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:66420800-66451800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr17:66425400-66451600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:66425400-66452000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:66426000-66445400	Weak transcription	Brain Germinal Matrix	brain
7	chr17:66429800-66444200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:66430800-66444200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:66432000-66440400	Weak transcription	Brain Anterior Caudate	brain
10	chr17:66432000-66442200	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:66432200-66452400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:66432400-66446400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:66432600-66444200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:66432600-66451600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:66432800-66448200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:66433000-66442800	Weak transcription	NHEK	skin
17	chr17:66433000-66444400	Weak transcription	HMEC	breast
18	chr17:66433000-66451800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:66433000-66451800	Weak transcription	Hela-S3	cervix
20	chr17:66433600-66440200	Weak transcription	Gastric	stomach
21	chr17:66434400-66441600	Strong transcription	NH-A	brain
22	chr17:66434400-66447800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:66434400-66450200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:66434600-66442000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr17:66434600-66449000	Weak transcription	Thymus	Thymus
26	chr17:66434600-66450400	Strong transcription	Osteobl	bone
27	chr17:66434800-66441600	Weak transcription	Pancreas	Pancrea
28	chr17:66434800-66445400	Weak transcription	Esophagus	oesophagus
29	chr17:66434800-66452200	Weak transcription	Dnd41	blood
30	chr17:66434800-66452400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr17:66434800-66452600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr17:66435200-66452200	Weak transcription	Stomach Mucosa	stomach
33	chr17:66435600-66449400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:66435800-66447600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr17:66436000-66449000	Strong transcription	NHLF	lung
36	chr17:66436400-66439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:66436400-66445400	Weak transcription	Brain Angular Gyrus	brain
38	chr17:66436600-66440000	Enhancers	Fetal Heart	heart
39	chr17:66436800-66440400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:66437000-66439800	Genic enhancers	Adipose Nuclei	Adipose
41	chr17:66437000-66440600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr17:66437000-66440800	Genic enhancers	Left Ventricle	heart
43	chr17:66437000-66442200	Strong transcription	Ovary	ovary
44	chr17:66437200-66440600	Genic enhancers	Fetal Muscle Leg	muscle
45	chr17:66437200-66447000	Strong transcription	HepG2	liver
46	chr17:66437200-66451600	Weak transcription	GM12878-XiMat	blood
47	chr17:66437400-66442000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr17:66437400-66442600	Weak transcription	HSMM	muscle
49	chr17:66437400-66451600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:66437400-66451600	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links