Variant report

Variant	rs9568642
Chromosome Location	chr13:52192689-52192690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12856726	0.95[MEX][hapmap];0.81[TSI][hapmap]
rs4943008	0.83[MEX][hapmap]
rs6561644	0.87[MEX][hapmap]
rs7327107	0.87[MEX][hapmap]
rs7984225	0.87[MEX][hapmap]
rs7990679	0.87[MEX][hapmap]
rs9285179	0.83[MEX][hapmap]
rs9526792	0.87[MEX][hapmap]
rs9535713	0.89[GIH][hapmap]
rs9535762	0.82[ASW][hapmap]
rs992583	0.87[MEX][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9568642	SLC34A2	trans	cerebellum	SCAN
rs9568642	VPS36	cis	cerebellum	SCAN
rs9568642	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52168400-52194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:52182200-52194400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:52184400-52194400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:52186800-52193000	Weak transcription	HepG2	liver
5	chr13:52187400-52194000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:52188800-52192800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr13:52188800-52192800	Weak transcription	Fetal Brain Female	brain
8	chr13:52188800-52192800	Weak transcription	Right Atrium	heart
9	chr13:52188800-52192800	Weak transcription	Right Ventricle	heart
10	chr13:52188800-52193000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:52188800-52193000	Weak transcription	Esophagus	oesophagus
12	chr13:52188800-52193800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr13:52188800-52194000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr13:52188800-52194400	Weak transcription	Fetal Brain Male	brain
15	chr13:52188800-52195800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:52188800-52197000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:52188800-52199200	Weak transcription	Liver	Liver
18	chr13:52189000-52192800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:52189000-52192800	Weak transcription	Fetal Muscle Leg	muscle
20	chr13:52189000-52192800	Weak transcription	Gastric	stomach
21	chr13:52189000-52193000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr13:52189000-52193000	Weak transcription	Left Ventricle	heart
23	chr13:52189000-52193400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:52189000-52194000	Weak transcription	Aorta	Aorta
25	chr13:52189000-52194400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:52189000-52194400	Weak transcription	Lung	lung
27	chr13:52189000-52194400	Weak transcription	Spleen	Spleen
28	chr13:52189000-52197400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:52189000-52197800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:52189200-52193000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:52189200-52193200	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:52189200-52194400	Weak transcription	Adipose Nuclei	Adipose
33	chr13:52189200-52194600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:52189200-52194600	Weak transcription	Psoas Muscle	Psoas
35	chr13:52189200-52194600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr13:52189200-52194600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr13:52189200-52195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:52189200-52196200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:52189200-52196200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:52189200-52197200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr13:52189400-52192800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:52189400-52193000	Weak transcription	Primary T cells from cord blood	blood
43	chr13:52189400-52193200	Weak transcription	GM12878-XiMat	blood
44	chr13:52189400-52197200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr13:52189400-52197200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr13:52189400-52205600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:52189400-52206600	Weak transcription	Primary B cells from cord blood	blood
48	chr13:52189400-52208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr13:52190400-52192800	Weak transcription	Pancreas	Pancrea
50	chr13:52190400-52196200	Enhancers	Fetal Heart	heart

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