Variant report

Variant	rs9609299
Chromosome Location	chr22:31894237-31894238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31892596..31895248-chr22:31897166..31900535,3	MCF-7	breast:
2	chr22:31892881..31894794-chr22:31897314..31900016,2	K562	blood:
3	chr22:31892695..31894776-chr22:32016253..32018919,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13057504	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2273249	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2273251	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34538851	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749267	0.80[AMR][1000 genomes]
rs5749268	0.80[AMR][1000 genomes]
rs5749270	0.80[AMR][1000 genomes]
rs5749283	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749286	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749291	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749295	0.81[ASN][1000 genomes]
rs5749298	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753610	0.80[AMR][1000 genomes]
rs5753613	0.80[AMR][1000 genomes]
rs5753615	0.84[AMR][1000 genomes]
rs5753621	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753628	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753631	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753648	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753659	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753661	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753664	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753665	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753666	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753669	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753671	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5994394	0.80[AMR][1000 genomes]
rs7284622	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7285619	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8139625	0.84[AMR][1000 genomes]
rs8142121	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606839	0.80[AMR][1000 genomes]
rs9606843	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9606846	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606847	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606848	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606852	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609286	0.84[AMR][1000 genomes]
rs9609295	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609296	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609297	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609301	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609303	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609304	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3334530	chr22:31889221-31909085	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1059314	chr22:31893613-31936088	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9609299	SFI1	cis	Thyroid	GTEx
rs9609299	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893000-31905200	Weak transcription	Aorta	Aorta
2	chr22:31893200-31903600	Weak transcription	Left Ventricle	heart
3	chr22:31893200-31912200	Weak transcription	Small Intestine	intestine
4	chr22:31893200-31934800	Weak transcription	Ovary	ovary
5	chr22:31893400-31896600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:31893400-31897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:31893400-31900000	Weak transcription	HSMM	muscle
8	chr22:31893400-31905200	Weak transcription	Fetal Intestine Large	intestine
9	chr22:31893400-31907200	Weak transcription	Fetal Intestine Small	intestine
10	chr22:31893400-31909000	Weak transcription	Liver	Liver
11	chr22:31893400-31920400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr22:31893600-31894400	Enhancers	Primary B cells from cord blood	blood
14	chr22:31893600-31899800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr22:31893600-31900000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:31893600-31900000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr22:31893600-31900000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr22:31893600-31900000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:31893600-31900000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr22:31893600-31900000	Weak transcription	NHDF-Ad	bronchial
21	chr22:31893600-31904600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:31893600-31904600	Weak transcription	A549	lung
23	chr22:31893600-31904800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr22:31893600-31907000	Weak transcription	Lung	lung
25	chr22:31893600-31909000	Weak transcription	Fetal Brain Male	brain
26	chr22:31893600-31925600	Weak transcription	Gastric	stomach
27	chr22:31893600-31926200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:31893600-31928200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:31893600-31934800	Weak transcription	Pancreas	Pancrea
30	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
32	chr22:31893800-31894400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr22:31893800-31894800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:31893800-31894800	Weak transcription	Fetal Thymus	thymus
35	chr22:31893800-31895200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr22:31893800-31895200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:31893800-31895600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:31893800-31896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr22:31893800-31897800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:31893800-31897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr22:31893800-31897800	Weak transcription	Spleen	Spleen
42	chr22:31893800-31899000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr22:31893800-31900600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:31893800-31904800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr22:31893800-31907000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr22:31893800-31907400	Weak transcription	Right Ventricle	heart
47	chr22:31893800-31913400	Weak transcription	Fetal Muscle Leg	muscle
48	chr22:31893800-31914600	Weak transcription	HepG2	liver
49	chr22:31893800-31921800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr22:31893800-31924600	Weak transcription	Adipose Nuclei	Adipose

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