Variant report

Variant	rs2729375
Chromosome Location	chr11:57330767-57330768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57297426..57300384-chr11:57328449..57331684,3	K562	blood:

Variant related genes	Relation type
ENSG00000134809	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1124942	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12223229	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234409	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2467328	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2467329	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2467330	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2581930	0.81[EUR][1000 genomes]
rs2649644	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649645	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649649	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649651	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649653	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2649655	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649656	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649658	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649659	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649666	0.86[EUR][1000 genomes]
rs2729358	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729359	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729367	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729368	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729369	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729370	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729373	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729382	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2848621	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2848622	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848624	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2848638	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2848639	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs514385	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs722823	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2729375	SMTNL1	cis	Nerve Tibial	GTEx
rs2729375	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729375	SMTNL1	cis	Thyroid	GTEx
rs2729375	SMTNL1	cis	Artery Tibial	GTEx
rs2729375	SMTNL1	cis	lung	GTEx
rs2729375	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs2729375	SMTNL1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
2	chr11:57307200-57333600	Weak transcription	HMEC	breast
3	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
4	chr11:57315800-57330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:57320600-57333400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:57320600-57334800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:57320800-57332800	Weak transcription	Stomach Mucosa	stomach
8	chr11:57321000-57333400	Weak transcription	HepG2	liver
9	chr11:57322000-57334600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:57322200-57333200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:57322200-57333400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:57322200-57333400	Weak transcription	HSMMtube	muscle
13	chr11:57322200-57333600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:57322200-57333600	Weak transcription	Right Ventricle	heart
15	chr11:57322800-57333400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:57323000-57333200	Weak transcription	NHDF-Ad	bronchial
17	chr11:57323800-57333800	Weak transcription	Aorta	Aorta
18	chr11:57324000-57334000	Weak transcription	Pancreas	Pancrea
19	chr11:57324400-57333800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:57324800-57332800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:57324800-57333200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:57326400-57332800	Weak transcription	Brain Substantia Nigra	brain
23	chr11:57326400-57333600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:57326600-57332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:57326600-57332800	Weak transcription	Brain Anterior Caudate	brain
26	chr11:57326600-57333200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:57326600-57333200	Weak transcription	Fetal Lung	lung
28	chr11:57326600-57333400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:57326600-57333400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:57326800-57332800	Weak transcription	Colonic Mucosa	Colon
31	chr11:57326800-57332800	Weak transcription	Thymus	Thymus
32	chr11:57326800-57333000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:57326800-57333000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:57326800-57333000	Weak transcription	Fetal Brain Male	brain
35	chr11:57326800-57333000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:57326800-57333200	Weak transcription	Osteobl	bone
37	chr11:57326800-57333600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:57326800-57333600	Weak transcription	Fetal Kidney	kidney
39	chr11:57326800-57333600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:57326800-57333600	Weak transcription	Ovary	ovary
41	chr11:57326800-57333800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:57326800-57334000	Weak transcription	Esophagus	oesophagus
43	chr11:57327000-57332800	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:57327000-57333000	Weak transcription	Brain Angular Gyrus	brain
45	chr11:57327000-57333000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:57327000-57333200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:57327000-57333200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:57327000-57333400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:57327000-57333800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:57327000-57334000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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