Variant report

Variant	rs9748497
Chromosome Location	chr18:9396995-9396996
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	chr18:9393548..9395841-chr18:9396684..9399360,2	K562	blood:
2	chr18:9396886..9398786-chr18:9399883..9402900,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11875065	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12456325	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12457923	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12458365	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16954989	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16954996	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34741369	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4343349	0.80[EUR][1000 genomes]
rs4503865	0.82[EUR][1000 genomes]
rs4797368	0.82[EUR][1000 genomes]
rs55637024	0.82[EUR][1000 genomes]
rs56124420	0.82[EUR][1000 genomes]
rs56349417	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57333366	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57456386	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62087465	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62087466	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62087468	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62087472	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62087494	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6506663	0.82[EUR][1000 genomes]
rs7229150	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7233757	0.88[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7243117	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs8088103	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8089405	0.86[EUR][1000 genomes]
rs8093378	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8093683	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9676006	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9748605	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9962807	0.82[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9748497	TWSG1	cis	Esophagus Muscularis	GTEx
rs9748497	TWSG1	Cis_1M	lymphoblastoid	RTeQTL
rs9748497	TWSG1	cis	Esophagus Mucosa	GTEx
rs9748497	TWSG1	cis	Thyroid	GTEx
rs9748497	TWSG1	cis	Artery Tibial	GTEx
rs9748497	TWSG1	cis	Muscle Skeletal	GTEx
rs9748497	TWSG1	cis	normal skin	skin_eQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
3	chr18:9360400-9403000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr18:9364800-9409400	Weak transcription	Aorta	Aorta
5	chr18:9366600-9406000	Weak transcription	Esophagus	oesophagus
6	chr18:9366800-9397000	Weak transcription	NHEK	skin
7	chr18:9368400-9397200	Weak transcription	Placenta	Placenta
8	chr18:9381200-9399400	Weak transcription	Colon Smooth Muscle	Colon
9	chr18:9381400-9404600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:9387200-9403600	Weak transcription	K562	blood
11	chr18:9388200-9402800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr18:9388600-9404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr18:9388800-9402600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:9388800-9413200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr18:9389000-9403800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr18:9389400-9405400	Weak transcription	Lung	lung
17	chr18:9390200-9397200	Weak transcription	Small Intestine	intestine
18	chr18:9390400-9404400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr18:9390800-9404800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:9391000-9403800	Weak transcription	Gastric	stomach
21	chr18:9391400-9404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:9391600-9400200	Weak transcription	NHLF	lung
23	chr18:9392000-9400000	Weak transcription	HUVEC	blood vessel
24	chr18:9392000-9401200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr18:9392000-9403800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr18:9392200-9397200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:9392200-9398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr18:9392200-9401000	Weak transcription	Brain Substantia Nigra	brain
29	chr18:9392200-9401200	Weak transcription	Fetal Intestine Large	intestine
30	chr18:9392200-9403400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:9392200-9404400	Weak transcription	Adipose Nuclei	Adipose
32	chr18:9392400-9398600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr18:9392400-9400400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:9392400-9404600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr18:9392400-9404600	Weak transcription	Brain Hippocampus Middle	brain
36	chr18:9392600-9397000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr18:9392600-9398800	Weak transcription	Fetal Heart	heart
38	chr18:9392600-9400200	Weak transcription	Brain Angular Gyrus	brain
39	chr18:9392800-9401200	Weak transcription	Dnd41	blood
40	chr18:9392800-9402600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr18:9393000-9399800	Weak transcription	Fetal Kidney	kidney
42	chr18:9393000-9401800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr18:9393200-9397800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr18:9393200-9411400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr18:9393400-9407600	Weak transcription	Brain Germinal Matrix	brain
46	chr18:9393600-9404000	Weak transcription	Primary B cells from cord blood	blood
47	chr18:9393800-9399200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr18:9393800-9399600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:9394000-9397600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr18:9394000-9397800	Strong transcription	HSMM	muscle

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