Variant report

Variant	rs59749117
Chromosome Location	chr11:74070798-74070799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11236056	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236057	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12416880	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417457	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417458	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417835	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418387	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421595	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36014178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57858196	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58030284	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58206408	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58557652	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59325091	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59848587	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610828	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60721424	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61026077	1.00[ASN][1000 genomes]
rs61109636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1049915	chr11:74052264-74126319	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
7	nsv975949	chr11:74064143-74070893	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59749117	PGM2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74037400-74078800	Weak transcription	Small Intestine	intestine
3	chr11:74037800-74086200	Weak transcription	Brain Anterior Caudate	brain
4	chr11:74038000-74071200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:74038000-74077400	Weak transcription	Psoas Muscle	Psoas
6	chr11:74038000-74077600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:74038000-74084400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:74038200-74071000	Weak transcription	Fetal Stomach	stomach
9	chr11:74038200-74071400	Weak transcription	Left Ventricle	heart
10	chr11:74038200-74071400	Weak transcription	Lung	lung
11	chr11:74038200-74082000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:74038200-74084400	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:74038400-74084400	Weak transcription	Liver	Liver
14	chr11:74038400-74086200	Weak transcription	Adipose Nuclei	Adipose
15	chr11:74038600-74071400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:74039400-74071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:74041800-74071200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:74041800-74071400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:74042000-74077600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:74042200-74081200	Weak transcription	Hela-S3	cervix
21	chr11:74044800-74079200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr11:74045800-74071400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr11:74045800-74073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:74046000-74071800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:74047200-74071200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:74047800-74077600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:74048000-74070800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:74048400-74077800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:74049400-74071800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:74049400-74080400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:74049600-74070800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:74049800-74077400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:74050400-74070800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:74050800-74071000	Weak transcription	Fetal Intestine Small	intestine
35	chr11:74050800-74085800	Weak transcription	Colonic Mucosa	Colon
36	chr11:74051000-74071400	Weak transcription	Gastric	stomach
37	chr11:74051000-74071400	Weak transcription	Pancreas	Pancrea
38	chr11:74051200-74070800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:74052400-74071000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:74052400-74071200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:74053200-74071400	Weak transcription	Ovary	ovary
42	chr11:74053400-74071600	Weak transcription	Fetal Muscle Leg	muscle
43	chr11:74053600-74070800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:74054200-74071000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:74056200-74070800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:74056600-74070800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:74056600-74071400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:74056600-74077600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:74056800-74077400	Weak transcription	HSMMtube	muscle
50	chr11:74057200-74071200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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