Variant report

Variant	rs2066587
Chromosome Location	chr13:50685954-50685955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50670793..50672422-chr13:50683586..50685968,2	K562	blood:
2	chr13:50657825..50659478-chr13:50684121..50686082,2	K562	blood:
3	chr13:50679888..50682383-chr13:50685487..50687936,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1326120	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2066558	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2066572	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066591	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066594	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2687950	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2740508	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2803839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812204	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812216	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812217	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2997624	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4942899	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap]
rs4942901	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap]
rs9535407	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs9568354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs9568357	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs9568363	0.89[AMR][1000 genomes]
rs9568364	0.89[AMR][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs9596215	0.88[AMR][1000 genomes]
rs9596219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9596220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2066587	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2066587	KCNRG	cis	cerebellum	SCAN
rs2066587	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs2066587	PHF11	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50658000-50697200	Weak transcription	HSMMtube	muscle
2	chr13:50659800-50697200	Weak transcription	Hela-S3	cervix
3	chr13:50671600-50689800	Weak transcription	Colonic Mucosa	Colon
4	chr13:50672000-50689400	Weak transcription	Right Ventricle	heart
5	chr13:50673000-50695600	Weak transcription	Fetal Intestine Large	intestine
6	chr13:50673600-50688400	Weak transcription	HepG2	liver
7	chr13:50673600-50690400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:50673800-50693800	Weak transcription	K562	blood
9	chr13:50673800-50697600	Weak transcription	HSMM	muscle
10	chr13:50674000-50689400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:50674000-50689400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:50674000-50689600	Weak transcription	Aorta	Aorta
13	chr13:50674000-50693800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:50674000-50695000	Weak transcription	Fetal Muscle Leg	muscle
15	chr13:50674000-50695400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr13:50674000-50695600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:50674000-50697200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:50674000-50697600	Weak transcription	Esophagus	oesophagus
19	chr13:50674200-50689400	Weak transcription	Left Ventricle	heart
20	chr13:50674200-50695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:50674600-50695400	Weak transcription	Fetal Intestine Small	intestine
22	chr13:50676800-50695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:50678000-50689600	Weak transcription	Liver	Liver
24	chr13:50679200-50688800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:50679200-50697200	Weak transcription	NH-A	brain
26	chr13:50679400-50688600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:50679400-50691000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:50680800-50689000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr13:50681400-50693800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:50681400-50697200	Weak transcription	Fetal Kidney	kidney
31	chr13:50681600-50688400	Weak transcription	Fetal Lung	lung
32	chr13:50681600-50689600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:50681800-50688400	Weak transcription	Brain Hippocampus Middle	brain
34	chr13:50681800-50691000	Weak transcription	Osteobl	bone
35	chr13:50682000-50687200	Weak transcription	Psoas Muscle	Psoas
36	chr13:50682000-50688400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:50682000-50688600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr13:50682000-50688600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr13:50682000-50688800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr13:50682000-50689200	Weak transcription	Adipose Nuclei	Adipose
41	chr13:50682000-50689200	Weak transcription	Thymus	Thymus
42	chr13:50682000-50689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:50682000-50692000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:50682000-50694600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr13:50682000-50697200	Weak transcription	NHDF-Ad	bronchial
46	chr13:50682200-50687800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:50682200-50688800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:50682200-50689400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr13:50682200-50690600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr13:50682200-50692200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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