Variant report

Variant	rs9568363
Chromosome Location	chr13:50531767-50531768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50531429..50533687-chr13:50538625..50541399,2	K562	blood:
2	chr13:50531043..50532904-chr13:50944878..50946623,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs1326120	0.88[AMR][1000 genomes]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2066558	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066572	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2066575	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs2066587	0.89[AMR][1000 genomes]
rs2066591	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2066594	0.91[AMR][1000 genomes]
rs2242482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2475837	0.82[ASN][1000 genomes]
rs2687950	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs2740508	0.91[AMR][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2740544	1.00[CEU][hapmap];0.95[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];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2760914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2803839	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2812204	0.85[AMR][1000 genomes]
rs2812216	0.89[AMR][1000 genomes]
rs2812217	0.89[AMR][1000 genomes]
rs2812222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs2997624	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4942899	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942901	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336058	0.91[ASN][1000 genomes]
rs7338055	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73489861	0.81[ASN][1000 genomes]
rs73489862	0.81[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap]
rs7986337	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs9535407	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9568354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs9568364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs9596215	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596219	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596220	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
3	nsv561630	chr13:50525141-50545402	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9568363	DLEU2	cis	multi-tissue	Pritchard
rs9568363	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs9568363	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs9568363	PHF11	cis	cerebellum	SCAN
rs9568363	KCNRG	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
2	chr13:50513400-50532600	Weak transcription	Ovary	ovary
3	chr13:50513400-50532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:50525800-50532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr13:50529400-50534000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr13:50529400-50547000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr13:50529600-50537000	Weak transcription	Psoas Muscle	Psoas
9	chr13:50529600-50550000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr13:50529800-50532600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:50529800-50536600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:50529800-50539400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:50529800-50543200	Weak transcription	Osteobl	bone
14	chr13:50529800-50544800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:50530000-50536400	Weak transcription	Placenta	Placenta
16	chr13:50530000-50546600	Weak transcription	Fetal Thymus	thymus
17	chr13:50530400-50537200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr13:50530600-50533000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr13:50530800-50533200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:50531000-50531800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:50531200-50532800	Enhancers	Brain Substantia Nigra	brain
22	chr13:50531200-50533200	Enhancers	Brain Hippocampus Middle	brain
23	chr13:50531400-50532200	Enhancers	Brain Cingulate Gyrus	brain
24	chr13:50531400-50533000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:50531400-50533000	Enhancers	Brain Anterior Caudate	brain
26	chr13:50531400-50536000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:50531400-50550400	Weak transcription	NHDF-Ad	bronchial
28	chr13:50531600-50531800	ZNF genes & repeats	Aorta	Aorta
29	chr13:50531600-50532200	Strong transcription	Fetal Muscle Leg	muscle

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