Variant report

Variant	rs9535716
Chromosome Location	chr13:52181725-52181726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52175306..52178787-chr13:52179968..52182908,3	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1885855	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1923874	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4456399	0.81[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4533167	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943008	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943014	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6561644	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7320201	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7327107	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7984225	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7988297	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7990679	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9285179	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526792	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9535720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992583	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535716	FLJ13639	cis	multi-tissue	Pritchard
rs9535716	THSD1P1	cis	cerebellum	SCAN
rs9535716	WDFY2	cis	multi-tissue	Pritchard
rs9535716	WDFY2	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52163200-52182600	Weak transcription	Ovary	ovary
2	chr13:52165600-52188600	Weak transcription	Fetal Stomach	stomach
3	chr13:52168400-52194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:52169800-52187000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52169800-52188600	Weak transcription	Esophagus	oesophagus
6	chr13:52169800-52188600	Weak transcription	Gastric	stomach
7	chr13:52173600-52190400	Weak transcription	Fetal Heart	heart
8	chr13:52174200-52183000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:52174200-52188200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr13:52174400-52188400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:52174600-52183000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:52175000-52183000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr13:52175000-52183000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:52175000-52187200	Weak transcription	Spleen	Spleen
15	chr13:52175000-52188600	Weak transcription	Fetal Muscle Leg	muscle
16	chr13:52176000-52188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:52176200-52184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr13:52176600-52183000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr13:52176600-52188400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:52176600-52188400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:52176800-52181800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr13:52177000-52182600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:52177000-52182600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:52177000-52188400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:52177600-52182400	Weak transcription	Right Ventricle	heart
26	chr13:52177600-52182600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr13:52177600-52183000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr13:52178000-52182000	Weak transcription	Primary T cells from cord blood	blood
29	chr13:52178200-52188600	Weak transcription	Left Ventricle	heart
30	chr13:52178200-52188600	Weak transcription	Lung	lung
31	chr13:52179400-52183000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr13:52179400-52187200	Weak transcription	Pancreas	Pancrea
33	chr13:52179600-52181800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr13:52179600-52187200	Weak transcription	Right Atrium	heart
35	chr13:52180000-52181800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:52180000-52187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:52180200-52183000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:52180200-52183200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr13:52180200-52185800	Weak transcription	Psoas Muscle	Psoas
40	chr13:52180200-52186000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:52180400-52183000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:52180400-52183000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:52180400-52183000	Weak transcription	Brain Substantia Nigra	brain
44	chr13:52180400-52183200	Weak transcription	Brain Anterior Caudate	brain
45	chr13:52180400-52185200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:52180400-52186400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:52180600-52183000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:52180600-52183000	Weak transcription	Brain Angular Gyrus	brain
49	chr13:52180600-52183000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr13:52180600-52184000	Weak transcription	Brain Hippocampus Middle	brain

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