Variant report

Variant	rs62087466
Chromosome Location	chr18:9343987-9343988
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9341334..9344223-chr18:9346131..9348599,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11875065	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12456325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12457923	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12458365	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16954989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16954996	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34741369	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56349417	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57333366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57456386	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62087465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62087468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62087472	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62087494	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7229150	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7233757	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7243117	0.82[EUR][1000 genomes]
rs8088103	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8089405	0.82[EUR][1000 genomes]
rs8093378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8093683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9676006	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9748497	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9748605	0.93[AMR][1000 genomes];0.89[EUR][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	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	nsv458023	chr18:9240413-9357786	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv576447	chr18:9240413-9357786	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
rs62087466	TWSG1	cis	Esophagus Muscularis	GTEx
rs62087466	TWSG1	cis	Thyroid	GTEx
rs62087466	TWSG1	cis	Muscle Skeletal	GTEx
rs62087466	TWSG1	cis	Esophagus Mucosa	GTEx
rs62087466	TWSG1	cis	Artery Tibial	GTEx
rs62087466	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9335400-9347800	Weak transcription	Small Intestine	intestine
2	chr18:9335400-9369400	Weak transcription	Pancreas	Pancrea
3	chr18:9335400-9371400	Weak transcription	Gastric	stomach
4	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
5	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr18:9335800-9344000	Weak transcription	Esophagus	oesophagus
7	chr18:9335800-9345200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr18:9335800-9348000	Weak transcription	Psoas Muscle	Psoas
9	chr18:9335800-9348200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr18:9335800-9348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:9335800-9348400	Weak transcription	Thymus	Thymus
12	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
15	chr18:9335800-9367600	Weak transcription	Lung	lung
16	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
17	chr18:9336000-9346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr18:9336000-9348000	Weak transcription	Hela-S3	cervix
19	chr18:9336000-9348400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr18:9336000-9348400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr18:9336000-9348600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
24	chr18:9336200-9346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr18:9336200-9347600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr18:9336200-9348000	Weak transcription	HepG2	liver
27	chr18:9336200-9348200	Weak transcription	HMEC	breast
28	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
29	chr18:9336400-9349400	Weak transcription	Fetal Intestine Small	intestine
30	chr18:9337200-9346400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr18:9337200-9346800	Strong transcription	Fetal Muscle Leg	muscle
32	chr18:9337400-9345000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr18:9337600-9347600	Strong transcription	HSMM	muscle
34	chr18:9337800-9345600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:9338000-9345400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr18:9338200-9345800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr18:9338200-9348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr18:9338200-9354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr18:9338400-9346600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr18:9338400-9348200	Weak transcription	K562	blood
41	chr18:9338400-9348200	Weak transcription	NHEK	skin
42	chr18:9338400-9348400	Weak transcription	Stomach Mucosa	stomach
43	chr18:9338400-9361600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr18:9338400-9366200	Weak transcription	Brain Anterior Caudate	brain
45	chr18:9338600-9344200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:9338800-9348000	Weak transcription	Colon Smooth Muscle	Colon
47	chr18:9338800-9366000	Weak transcription	Brain Hippocampus Middle	brain
48	chr18:9339600-9347600	Weak transcription	HUVEC	blood vessel
49	chr18:9339600-9365600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr18:9340600-9344200	Strong transcription	Dnd41	blood

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