Variant report

Variant	rs9568650
Chromosome Location	chr13:52253655-52253656
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52251709..52254335-chr13:52256539..52260633,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1024271	0.95[JPT][hapmap]
rs12585249	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs17075881	1.00[YRI][hapmap]
rs17075900	1.00[YRI][hapmap]
rs17075902	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[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075628	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs4625625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4941703	0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs4941710	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943005	0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs4943009	0.89[GIH][hapmap]
rs4943018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328695	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7332603	1.00[YRI][hapmap]
rs7332922	0.82[YRI][hapmap]
rs7333623	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745374	0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs7986066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993522	1.00[YRI][hapmap]
rs9316547	0.90[JPT][hapmap]
rs9316551	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9563063	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs9563065	0.88[ASN][1000 genomes]
rs9563066	0.89[ASN][1000 genomes]
rs9563067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568644	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9568647	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568649	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568658	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805172	0.84[CHB][hapmap];0.95[JPT][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9568650	WDFY2	cis	parietal	SCAN
rs9568650	TRIM13	cis	cerebellum	SCAN
rs9568650	MANF	trans	parietal	SCAN
rs9568650	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52219600-52253800	Weak transcription	Psoas Muscle	Psoas
2	chr13:52220400-52259000	Weak transcription	Thymus	Thymus
3	chr13:52221200-52253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:52228600-52254000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52232200-52261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:52232800-52256400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:52234000-52277800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:52234200-52258800	Weak transcription	Adipose Nuclei	Adipose
9	chr13:52234200-52263200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:52234800-52257600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:52235200-52253800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:52237200-52257400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr13:52237200-52261400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:52237400-52254400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:52238600-52256800	Weak transcription	Fetal Muscle Leg	muscle
16	chr13:52238600-52259400	Weak transcription	Fetal Stomach	stomach
17	chr13:52239200-52257400	Weak transcription	Colon Smooth Muscle	Colon
18	chr13:52239200-52263200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr13:52240800-52254000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:52243400-52254000	Weak transcription	Dnd41	blood
21	chr13:52243400-52255800	Weak transcription	Fetal Intestine Small	intestine
22	chr13:52244400-52257000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:52244600-52257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:52244800-52262200	Weak transcription	Ovary	ovary
25	chr13:52247200-52277400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:52247400-52254400	Weak transcription	NH-A	brain
27	chr13:52247400-52257000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:52247600-52261600	Weak transcription	GM12878-XiMat	blood
29	chr13:52247600-52262000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
32	chr13:52247800-52254600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:52247800-52262200	Weak transcription	Spleen	Spleen
34	chr13:52248000-52254400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:52248400-52255000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:52248600-52257600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:52248800-52253800	Weak transcription	Pancreas	Pancrea
38	chr13:52248800-52254200	Weak transcription	Left Ventricle	heart
39	chr13:52248800-52257800	Weak transcription	Aorta	Aorta
40	chr13:52249000-52255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:52249000-52257600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr13:52249000-52257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:52249200-52255400	Strong transcription	Primary B cells from cord blood	blood
44	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr13:52249800-52257600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr13:52249800-52257600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr13:52249800-52258000	Weak transcription	Brain Substantia Nigra	brain
48	chr13:52249800-52261400	Weak transcription	Brain Anterior Caudate	brain
49	chr13:52249800-52262000	Weak transcription	Brain Angular Gyrus	brain
50	chr13:52250000-52254400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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