Variant report

Variant	rs9526788
Chromosome Location	chr13:52263834-52263835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12146894	1.00[JPT][hapmap]
rs12427748	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1475195	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1885854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2296029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2897944	1.00[JPT][hapmap]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs491103	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535699	1.00[ASW][hapmap]
rs9535714	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535734	0.80[ASN][1000 genomes]
rs9535735	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535738	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535744	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535748	1.00[JPT][hapmap]
rs9535749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535756	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.86[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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9526788	WDFY2	cis	parietal	SCAN
rs9526788	CKAP2	cis	parietal	SCAN
rs9526788	HNRNPA1L2	cis	parietal	SCAN
rs9526788	WDFY2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52234000-52277800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:52247200-52277400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
5	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:52251200-52269600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:52254400-52270200	Weak transcription	Esophagus	oesophagus
8	chr13:52254400-52273200	Weak transcription	Pancreas	Pancrea
9	chr13:52254600-52293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:52255400-52273200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:52255600-52273200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:52256400-52277800	Weak transcription	HSMMtube	muscle
14	chr13:52258000-52273400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:52258000-52280400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr13:52258600-52271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:52258600-52273400	Weak transcription	NHEK	skin
18	chr13:52258800-52270600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr13:52259200-52278000	Weak transcription	Primary T cells from cord blood	blood
20	chr13:52259400-52273200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr13:52259400-52277800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr13:52261000-52273800	Weak transcription	Primary B cells from cord blood	blood
23	chr13:52261400-52264200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:52261600-52264200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr13:52261600-52264200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr13:52261600-52264200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:52261600-52264200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:52261800-52264000	Enhancers	Fetal Brain Female	brain
29	chr13:52262000-52264000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:52262000-52264000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr13:52262000-52264200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:52262000-52264200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:52262000-52264200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr13:52262800-52264200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr13:52262800-52269400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr13:52263000-52264200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr13:52263000-52264200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:52263200-52264000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:52263200-52264000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:52263200-52264000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr13:52263200-52264000	Enhancers	Fetal Brain Male	brain
42	chr13:52263200-52264200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr13:52263200-52264200	Enhancers	Stomach Mucosa	stomach
44	chr13:52263200-52264200	Flanking Active TSS	GM12878-XiMat	blood
45	chr13:52263200-52264200	Enhancers	HMEC	breast
46	chr13:52263400-52264000	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr13:52263400-52264200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr13:52263400-52264200	Enhancers	K562	blood
49	chr13:52263400-52273200	Weak transcription	Gastric	stomach
50	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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