Variant report

Variant	rs2773350
Chromosome Location	chr9:100399132-100399133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10123528	1.00[JPT][hapmap]
rs10982745	0.85[CHD][hapmap]
rs16922598	1.00[JPT][hapmap]
rs1962592	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2149984	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2254733	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773343	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773349	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2773358	0.94[EUR][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.86[CEU][hapmap]
rs2805785	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2805786	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805787	0.89[EUR][1000 genomes]
rs2805788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805792	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805793	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.82[EUR][1000 genomes]
rs2805831	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805834	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2805835	1.00[JPT][hapmap]
rs2808669	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808676	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808682	1.00[JPT][hapmap]
rs7863516	0.88[ASN][1000 genomes]
rs932916	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3391802	chr9:100398381-100399579	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2773350	TMOD1	cis	cerebellum	SCAN
rs2773350	TBC1D2	cis	parietal	SCAN
rs2773350	ZNF367	cis	parietal	SCAN
rs2773350	C9orf89	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100394400-100399200	Active TSS	Right Atrium	heart
2	chr9:100394600-100399200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:100396800-100400600	Weak transcription	Gastric	stomach
4	chr9:100396800-100410200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:100397000-100399600	Enhancers	Stomach Mucosa	stomach
6	chr9:100397000-100403000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:100397000-100405800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:100397000-100409200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:100397000-100410200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:100397000-100410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:100397000-100411000	Weak transcription	Esophagus	oesophagus
12	chr9:100397200-100399400	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:100397200-100399400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr9:100397200-100399400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:100397200-100400000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr9:100397200-100400200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr9:100397200-100405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:100397400-100399400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:100397400-100399400	Enhancers	Small Intestine	intestine
20	chr9:100397400-100400000	Enhancers	Adipose Nuclei	Adipose
21	chr9:100397400-100401600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:100397400-100401800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr9:100397400-100402000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:100397400-100403000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr9:100397600-100399200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:100397600-100399400	Enhancers	Fetal Brain Male	brain
27	chr9:100397600-100399600	Enhancers	Brain Angular Gyrus	brain
28	chr9:100397600-100399800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:100397600-100399800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr9:100397600-100400000	Enhancers	NHDF-Ad	bronchial
31	chr9:100397600-100400800	Enhancers	Primary T cells from cord blood	blood
32	chr9:100397600-100401200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr9:100397600-100401600	Enhancers	Liver	Liver
34	chr9:100397600-100402000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr9:100397600-100403000	Weak transcription	Placenta	Placenta
36	chr9:100397600-100403800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:100397600-100405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:100397600-100405400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:100397600-100405400	Weak transcription	Fetal Kidney	kidney
40	chr9:100397600-100409800	Weak transcription	Colonic Mucosa	Colon
41	chr9:100397800-100399800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:100397800-100401000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:100397800-100405800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:100398000-100399800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:100398000-100400600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:100398000-100403200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:100398000-100410200	Weak transcription	Lung	lung
48	chr9:100398000-100418600	Weak transcription	Pancreas	Pancrea
49	chr9:100398200-100399200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr9:100398400-100399200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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