Variant report

Variant	rs62087468
Chromosome Location	chr18:9352071-9352072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9351096..9353244-chr18:9355745..9358612,2	K562	blood:
2	chr18:9351286..9353025-chr18:9353787..9355705,3	K562	blood:
3	chr18:9351096..9353244-chr18:9355745..9359443,3	K562	blood:
4	chr18:9334775..9336689-chr18:9351214..9352717,2	K562	blood:

Variant related genes	Relation type
ENSG00000128791	Chromatin interaction

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

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

rs_ID	r²[population]
rs11875065	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12456325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12457923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12458365	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16954989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16954996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34741369	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56349417	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57333366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57456386	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62087472	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62087494	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7229150	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7233757	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7243117	0.86[EUR][1000 genomes]
rs8088103	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8089405	0.83[EUR][1000 genomes]
rs8093378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8093683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9676006	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9748497	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9748605	0.93[AMR][1000 genomes];0.94[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
rs62087468	TWSG1	cis	Esophagus Mucosa	GTEx
rs62087468	TWSG1	cis	Esophagus Muscularis	GTEx
rs62087468	TWSG1	cis	Muscle Skeletal	GTEx
rs62087468	TWSG1	cis	Artery Tibial	GTEx
rs62087468	TWSG1	cis	Thyroid	GTEx
rs62087468	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9335400-9369400	Weak transcription	Pancreas	Pancrea
2	chr18:9335400-9371400	Weak transcription	Gastric	stomach
3	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
4	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
8	chr18:9335800-9367600	Weak transcription	Lung	lung
9	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
10	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
12	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
13	chr18:9338200-9354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:9338400-9361600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:9338400-9366200	Weak transcription	Brain Anterior Caudate	brain
16	chr18:9338800-9366000	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:9339600-9365600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr18:9341000-9371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:9341200-9361400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:9341200-9366400	Weak transcription	Brain Substantia Nigra	brain
21	chr18:9341200-9367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:9341200-9391400	Weak transcription	Liver	Liver
23	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:9341400-9366200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr18:9344000-9366000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr18:9344000-9367400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr18:9344200-9361400	Weak transcription	Brain Germinal Matrix	brain
28	chr18:9344200-9367600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr18:9344200-9367800	Weak transcription	Primary B cells from cord blood	blood
30	chr18:9344400-9360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
32	chr18:9344800-9360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr18:9345000-9361800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:9345200-9367400	Weak transcription	Fetal Brain Female	brain
35	chr18:9345600-9367000	Weak transcription	Fetal Intestine Large	intestine
36	chr18:9345600-9367400	Weak transcription	Placenta	Placenta
37	chr18:9345600-9377600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr18:9346600-9361400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr18:9346800-9361400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr18:9346800-9361400	Weak transcription	Fetal Muscle Leg	muscle
41	chr18:9348400-9353000	Weak transcription	Fetal Stomach	stomach
42	chr18:9348600-9353600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:9348600-9359000	Weak transcription	Ovary	ovary
44	chr18:9348600-9360600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr18:9348600-9360600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr18:9348600-9361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr18:9348600-9361400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:9348600-9362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr18:9348600-9365600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr18:9348600-9369600	Weak transcription	K562	blood

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