Variant report

Variant	rs17747599
Chromosome Location	chr22:34287350-34287351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34277917..34281628-chr22:34285820..34288664,3	MCF-7	breast:
2	chr22:34261283..34264105-chr22:34285527..34288136,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1005680	1.00[ASN][1000 genomes]
rs10483174	1.00[ASN][1000 genomes]
rs11703305	1.00[ASN][1000 genomes]
rs11704212	1.00[ASN][1000 genomes]
rs11705063	1.00[ASN][1000 genomes]
rs11912301	1.00[ASN][1000 genomes]
rs11912405	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11913804	1.00[ASN][1000 genomes]
rs11914012	0.93[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130523	1.00[ASN][1000 genomes]
rs13055480	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16993078	1.00[ASN][1000 genomes]
rs16993089	1.00[ASN][1000 genomes]
rs2413206	1.00[ASN][1000 genomes]
rs2413208	1.00[ASN][1000 genomes]
rs34060203	1.00[ASN][1000 genomes]
rs34290110	1.00[ASN][1000 genomes]
rs34375307	1.00[ASN][1000 genomes]
rs34455747	1.00[ASN][1000 genomes]
rs34597805	1.00[ASN][1000 genomes]
rs34871405	1.00[ASN][1000 genomes]
rs35838699	1.00[ASN][1000 genomes]
rs36006309	1.00[ASN][1000 genomes]
rs55819147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963330	1.00[ASN][1000 genomes]
rs5749698	1.00[ASN][1000 genomes]
rs5754739	1.00[ASN][1000 genomes]
rs5754746	1.00[ASN][1000 genomes]
rs58634529	1.00[ASN][1000 genomes]
rs5999089	1.00[ASN][1000 genomes]
rs67258059	1.00[ASN][1000 genomes]
rs73154536	1.00[ASN][1000 genomes]
rs73154574	1.00[ASN][1000 genomes]
rs73170572	1.00[ASN][1000 genomes]
rs73170587	1.00[ASN][1000 genomes]
rs73170592	1.00[ASN][1000 genomes]
rs73170593	1.00[ASN][1000 genomes]
rs73170600	1.00[ASN][1000 genomes]
rs73171909	1.00[ASN][1000 genomes]
rs73171910	1.00[ASN][1000 genomes]
rs73171912	1.00[ASN][1000 genomes]
rs73171913	1.00[ASN][1000 genomes]
rs73171915	1.00[ASN][1000 genomes]
rs73171921	1.00[ASN][1000 genomes]
rs73171926	1.00[ASN][1000 genomes]
rs73171927	1.00[ASN][1000 genomes]
rs73171931	1.00[ASN][1000 genomes]
rs738987	1.00[ASN][1000 genomes]
rs738989	1.00[ASN][1000 genomes]
rs933215	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv588938	chr22:34270568-34307875	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17747599	RBM9	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34271600-34287400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr22:34273200-34292200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr22:34274600-34291200	Enhancers	Fetal Heart	heart
4	chr22:34280000-34292200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:34280600-34289200	Weak transcription	Stomach Mucosa	stomach
6	chr22:34280800-34288200	Weak transcription	Ovary	ovary
7	chr22:34280800-34293200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:34281000-34287800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:34281000-34288000	Weak transcription	Gastric	stomach
10	chr22:34281000-34289800	Weak transcription	Pancreas	Pancrea
11	chr22:34281200-34289800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr22:34283000-34292000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr22:34284000-34288000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr22:34285000-34287400	Enhancers	Fetal Brain Male	brain
15	chr22:34285000-34292400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr22:34285400-34290800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr22:34285600-34287400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr22:34285600-34288400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr22:34285600-34290600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr22:34285800-34287400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr22:34285800-34287400	Weak transcription	Brain Anterior Caudate	brain
22	chr22:34286000-34290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:34286000-34291800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr22:34286200-34287800	Enhancers	GM12878-XiMat	blood
25	chr22:34286200-34288000	Weak transcription	Spleen	Spleen
26	chr22:34286200-34288200	Weak transcription	Psoas Muscle	Psoas
27	chr22:34286200-34288200	Weak transcription	Right Atrium	heart
28	chr22:34286200-34289200	Weak transcription	Fetal Brain Female	brain
29	chr22:34286200-34290400	Weak transcription	Esophagus	oesophagus
30	chr22:34286400-34290600	Weak transcription	Colon Smooth Muscle	Colon
31	chr22:34286400-34290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:34286400-34292200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr22:34286400-34296600	Weak transcription	Adipose Nuclei	Adipose
34	chr22:34286800-34287400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:34286800-34290600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr22:34287000-34288600	Enhancers	Fetal Lung	lung
37	chr22:34287000-34289800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:34287000-34290800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:34287200-34288600	Weak transcription	HepG2	liver
40	chr22:34287200-34289800	Weak transcription	Left Ventricle	heart
41	chr22:34287200-34289800	Weak transcription	Right Ventricle	heart
42	chr22:34287200-34291400	Weak transcription	Primary B cells from peripheral blood	blood

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