Variant report

Variant	rs17597531
Chromosome Location	chr13:52222222-52222223
allele	C/T
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	0.89[ASN][1000 genomes]
rs12146894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1475195	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];0.97[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17597215	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];0.85[EUR][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2897944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4555048	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]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs491103	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526786	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]
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];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535699	1.00[ASW][hapmap]
rs9535714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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];0.94[EUR][1000 genomes];0.83[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];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535734	0.89[ASN][1000 genomes]
rs9535735	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535739	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[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];0.85[EUR][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[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
rs17597531	FLJ13639	cis	multi-tissue	Pritchard
rs17597531	WDFY2	cis	multi-tissue	Pritchard
rs17597531	HNRNPA1L2	cis	parietal	SCAN
rs17597531	CKAP2	cis	parietal	SCAN
rs17597531	WDFY2	cis	cerebellum	SCAN
rs17597531	WDFY2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52217200-52222400	Enhancers	Brain Substantia Nigra	brain
2	chr13:52217400-52222400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr13:52217400-52222400	Enhancers	HepG2	liver
4	chr13:52217400-52222600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:52219600-52253800	Weak transcription	Psoas Muscle	Psoas
6	chr13:52219800-52233800	Weak transcription	A549	lung
7	chr13:52220200-52222400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:52220200-52222600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:52220400-52222400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr13:52220400-52259000	Weak transcription	Thymus	Thymus
11	chr13:52220600-52222800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:52220600-52223000	Weak transcription	Left Ventricle	heart
13	chr13:52220600-52223200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:52220600-52227600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:52220600-52228200	Weak transcription	Esophagus	oesophagus
16	chr13:52220600-52228400	Weak transcription	Lung	lung
17	chr13:52220600-52233400	Weak transcription	Ovary	ovary
18	chr13:52220600-52233400	Weak transcription	Right Atrium	heart
19	chr13:52220600-52236400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:52220800-52222400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr13:52220800-52223200	Weak transcription	Aorta	Aorta
22	chr13:52220800-52225400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr13:52220800-52229800	Weak transcription	Adipose Nuclei	Adipose
24	chr13:52220800-52233600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:52221000-52222400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:52221000-52222400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr13:52221000-52223600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:52221000-52225800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr13:52221000-52226000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:52221000-52227800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:52221000-52228000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:52221000-52229200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:52221000-52235800	Weak transcription	HSMM	muscle
34	chr13:52221200-52222400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr13:52221200-52228000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:52221200-52228000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:52221200-52228400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:52221200-52253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:52221400-52222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr13:52221400-52223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:52221400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:52221400-52228000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr13:52221600-52222600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr13:52221600-52222600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr13:52221600-52233400	Weak transcription	Osteobl	bone
46	chr13:52221600-52238000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr13:52221800-52222600	Enhancers	Brain Hippocampus Middle	brain
48	chr13:52221800-52222600	Strong transcription	NHEK	skin
49	chr13:52222000-52222400	Enhancers	Right Ventricle	heart
50	chr13:52222000-52222600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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