Variant report

Variant	rs356678
Chromosome Location	chr9:97991935-97991936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1045276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10491560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs10761381	0.83[CHB][hapmap]
rs171417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187172	1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes]
rs2282216	0.85[JPT][hapmap]
rs356666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356669	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs356673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356679	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356683	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356687	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs356688	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3780567	0.90[JPT][hapmap]
rs3824486	0.85[JPT][hapmap]
rs416792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs437511	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4647376	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4647534	0.90[JPT][hapmap]
rs4744451	0.90[JPT][hapmap]
rs526189	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540412	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs565293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs609324	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs657637	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7033633	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs944934	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs356678	PHF2	cis	cerebellum	SCAN
rs356678	NINJ1	cis	cerebellum	SCAN
rs356678	TDRD7	cis	cerebellum	SCAN
rs356678	SYK	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97963000-97993400	Weak transcription	Hela-S3	cervix
2	chr9:97973600-98024000	Weak transcription	Gastric	stomach
3	chr9:97974000-98009400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:97978000-98008400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:97978200-97994400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:97981400-97993800	Weak transcription	Esophagus	oesophagus
7	chr9:97981400-98012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:97981600-98009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:97983400-98012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:97984600-97999600	Weak transcription	Fetal Heart	heart
11	chr9:97987200-98015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:97987800-97993600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:97987800-97999600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:97987800-98008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:97988200-98007200	Weak transcription	Fetal Lung	lung
16	chr9:97988400-98012200	Weak transcription	Fetal Kidney	kidney
17	chr9:97988600-97993400	Weak transcription	A549	lung
18	chr9:97988600-97999600	Weak transcription	Aorta	Aorta
19	chr9:97989200-98009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:97989200-98012400	Weak transcription	Ovary	ovary
21	chr9:97989400-97995200	Weak transcription	HSMM	muscle
22	chr9:97989400-98012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:97989400-98013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:97989600-98006400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:97989600-98012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:97989800-97993200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:97989800-98007400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:97989800-98011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:97990000-97992400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:97990000-97992400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:97990200-98013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:97990400-98008200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:97990400-98012600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:97990800-97992800	Enhancers	Fetal Intestine Large	intestine
35	chr9:97990800-98001200	Weak transcription	Pancreas	Pancrea
36	chr9:97991000-97992000	Strong transcription	Fetal Stomach	stomach
37	chr9:97991000-98010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:97991200-97992200	Enhancers	HepG2	liver
39	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:97991600-97992000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:97991600-97992200	Enhancers	Fetal Intestine Small	intestine
42	chr9:97991600-97992600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97991800-97992600	Enhancers	Liver	Liver

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