Variant report

Variant	rs57456386
Chromosome Location	chr18:9390346-9390347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11875065	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12456325	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12457923	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12458365	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16954989	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16954996	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34741369	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4343349	0.83[EUR][1000 genomes]
rs4503865	0.84[EUR][1000 genomes]
rs4797368	0.84[EUR][1000 genomes]
rs55637024	0.84[EUR][1000 genomes]
rs56124420	0.84[EUR][1000 genomes]
rs56349417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57333366	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62087465	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62087466	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62087468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087472	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62087494	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6506663	0.84[EUR][1000 genomes]
rs7229150	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7233757	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7243117	0.83[EUR][1000 genomes]
rs8088103	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8089405	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8093378	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8093683	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9676006	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9748497	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9748605	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9962807	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv909365	chr18:9299538-9400422	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs57456386	TWSG1	cis	Artery Tibial	GTEx
rs57456386	TWSG1	cis	Thyroid	GTEx
rs57456386	TWSG1	cis	Esophagus Muscularis	GTEx
rs57456386	TWSG1	cis	Muscle Skeletal	GTEx
rs57456386	TWSG1	cis	Esophagus Mucosa	GTEx
rs57456386	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9341200-9391400	Weak transcription	Liver	Liver
2	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
4	chr18:9360400-9403000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr18:9364800-9409400	Weak transcription	Aorta	Aorta
6	chr18:9366600-9390600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:9366600-9390800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr18:9366600-9396200	Weak transcription	NH-A	brain
9	chr18:9366600-9406000	Weak transcription	Esophagus	oesophagus
10	chr18:9366800-9390600	Weak transcription	HUVEC	blood vessel
11	chr18:9366800-9397000	Weak transcription	NHEK	skin
12	chr18:9367800-9390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:9367800-9395600	Weak transcription	Left Ventricle	heart
14	chr18:9368200-9390400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr18:9368200-9390600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr18:9368400-9397200	Weak transcription	Placenta	Placenta
17	chr18:9368600-9390400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr18:9368600-9390400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr18:9370000-9390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:9380800-9390400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr18:9381000-9390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:9381200-9390400	Weak transcription	Fetal Muscle Leg	muscle
23	chr18:9381200-9391200	Weak transcription	Osteobl	bone
24	chr18:9381200-9391800	Weak transcription	HSMMtube	muscle
25	chr18:9381200-9399400	Weak transcription	Colon Smooth Muscle	Colon
26	chr18:9381400-9390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:9381400-9390600	Weak transcription	Brain Hippocampus Middle	brain
28	chr18:9381400-9390800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr18:9381400-9391200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr18:9381400-9391200	Weak transcription	NHDF-Ad	bronchial
31	chr18:9381400-9391400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:9381400-9391400	Weak transcription	Brain Anterior Caudate	brain
33	chr18:9381400-9391400	Weak transcription	Brain Substantia Nigra	brain
34	chr18:9381400-9395800	Weak transcription	Ovary	ovary
35	chr18:9381400-9404600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr18:9381800-9390400	Weak transcription	Brain Germinal Matrix	brain
37	chr18:9381800-9390600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:9382000-9390400	Weak transcription	Fetal Stomach	stomach
39	chr18:9382000-9390800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr18:9386400-9391800	Weak transcription	Adipose Nuclei	Adipose
41	chr18:9387200-9403600	Weak transcription	K562	blood
42	chr18:9387400-9390400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr18:9388200-9391400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:9388200-9402800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr18:9388600-9404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr18:9388800-9402600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr18:9388800-9413200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr18:9389000-9391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr18:9389000-9403800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:9389400-9390600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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