Variant report

Variant	rs9526786
Chromosome Location	chr13:52209422-52209423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1060562	0.86[ASN][1000 genomes]
rs12146894	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1475195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17532412	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885854	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];0.83[EUR][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897944	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs491103	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526788	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];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535699	1.00[ASW][hapmap]
rs9535714	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535717	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];0.86[ASN][1000 genomes]
rs9535722	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];0.86[ASN][1000 genomes]
rs9535734	0.86[ASN][1000 genomes]
rs9535735	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[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];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535746	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];0.83[EUR][1000 genomes]
rs9535747	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535748	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9526786	WDFY2	cis	parietal	SCAN
rs9526786	FLJ13639	cis	multi-tissue	Pritchard
rs9526786	CKAP2	cis	parietal	SCAN
rs9526786	WDFY2	cis	multi-tissue	Pritchard
rs9526786	HNRNPA1L2	cis	parietal	SCAN
rs9526786	WDFY2	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52194800-52217600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:52197600-52212400	Weak transcription	Fetal Kidney	kidney
3	chr13:52198600-52217600	Weak transcription	Fetal Thymus	thymus
4	chr13:52201200-52210800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:52202600-52210400	Weak transcription	Right Atrium	heart
6	chr13:52202800-52217600	Weak transcription	Fetal Stomach	stomach
7	chr13:52203000-52210800	Weak transcription	Right Ventricle	heart
8	chr13:52203000-52213600	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:52203400-52209600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:52205200-52212200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:52205200-52214600	Enhancers	Brain Substantia Nigra	brain
12	chr13:52207200-52209600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:52207200-52209600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:52207200-52212400	Weak transcription	Hela-S3	cervix
15	chr13:52207200-52212600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr13:52207200-52218400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:52207400-52210400	Weak transcription	Ovary	ovary
18	chr13:52207400-52210600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:52207400-52211200	Weak transcription	NHLF	lung
20	chr13:52207400-52212000	Weak transcription	Esophagus	oesophagus
21	chr13:52207600-52209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:52207600-52209600	Weak transcription	Left Ventricle	heart
23	chr13:52207600-52209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:52207600-52210000	Weak transcription	Gastric	stomach
25	chr13:52207600-52210000	Weak transcription	Pancreas	Pancrea
26	chr13:52207600-52210400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr13:52207600-52210400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr13:52207600-52210400	Weak transcription	Fetal Lung	lung
29	chr13:52207600-52210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr13:52207600-52210800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:52207600-52211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:52207600-52211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:52207600-52212000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:52207600-52212200	Weak transcription	HSMMtube	muscle
35	chr13:52207600-52214600	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:52207600-52217000	Weak transcription	Adipose Nuclei	Adipose
37	chr13:52207600-52220200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr13:52207800-52209600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr13:52207800-52209600	Weak transcription	NHEK	skin
40	chr13:52207800-52210400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:52207800-52210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:52207800-52210400	Weak transcription	HSMM	muscle
43	chr13:52207800-52210400	Weak transcription	NH-A	brain
44	chr13:52207800-52210400	Weak transcription	NHDF-Ad	bronchial
45	chr13:52207800-52210600	Weak transcription	Aorta	Aorta
46	chr13:52207800-52211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:52207800-52214600	Enhancers	Brain Hippocampus Middle	brain
48	chr13:52207800-52217400	Weak transcription	Brain Germinal Matrix	brain
49	chr13:52208000-52210200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:52208000-52210800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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