Variant report

Variant	rs1062359
Chromosome Location	chr18:9402174-9402175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9318662..9320883-chr18:9399469..9402396,2	K562	blood:
2	chr18:9400916..9402861-chr18:9404497..9406398,2	K562	blood:
3	chr18:9400579..9402356-chr18:9408633..9411407,2	K562	blood:
4	chr18:9401819..9404534-chr18:9474029..9476633,3	MCF-7	breast:
5	chr18:9396886..9398786-chr18:9399883..9402900,3	K562	blood:

Variant related genes	Relation type
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1074159	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11663997	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052039	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12959183	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12962166	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12963151	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12967229	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1605473	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1605474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1605476	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2298545	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2298550	0.81[ASN][1000 genomes]
rs35584133	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4797366	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4798797	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4798802	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4798804	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4798805	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4798806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4798808	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7228819	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7234330	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237136	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237485	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7239225	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7240798	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7242488	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7245034	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8085947	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8097838	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8099673	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965280	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9675975	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9944562	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9959183	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9963516	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9966961	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1062359	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr18:9381400-9404600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:9387200-9403600	Weak transcription	K562	blood
8	chr18:9388200-9402800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:9388600-9404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:9388800-9402600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:9388800-9413200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr18:9389000-9403800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr18:9389400-9405400	Weak transcription	Lung	lung
14	chr18:9390400-9404400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:9390800-9404800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr18:9391000-9403800	Weak transcription	Gastric	stomach
17	chr18:9391400-9404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:9392000-9403800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr18:9392200-9403400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:9392200-9404400	Weak transcription	Adipose Nuclei	Adipose
21	chr18:9392400-9404600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr18:9392400-9404600	Weak transcription	Brain Hippocampus Middle	brain
23	chr18:9392800-9402600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr18:9393200-9411400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr18:9393400-9407600	Weak transcription	Brain Germinal Matrix	brain
26	chr18:9393600-9404000	Weak transcription	Primary B cells from cord blood	blood
27	chr18:9394600-9402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:9394800-9402400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr18:9394800-9402800	Weak transcription	Fetal Brain Female	brain
30	chr18:9395000-9405600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr18:9395200-9403600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr18:9395400-9404200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr18:9395400-9404400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr18:9395600-9406000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:9396600-9413800	Weak transcription	NH-A	brain
36	chr18:9396800-9402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr18:9396800-9404200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr18:9397200-9413600	Weak transcription	HSMMtube	muscle
39	chr18:9397200-9416800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:9397400-9402400	Weak transcription	NHDF-Ad	bronchial
41	chr18:9397400-9403000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr18:9397400-9406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr18:9397600-9404600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr18:9397800-9402200	Weak transcription	GM12878-XiMat	blood
45	chr18:9397800-9403000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr18:9397800-9416600	Weak transcription	HSMM	muscle
47	chr18:9398400-9403600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr18:9398400-9404400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr18:9399000-9402400	Weak transcription	Fetal Stomach	stomach
50	chr18:9399000-9402600	Weak transcription	Fetal Muscle Leg	muscle

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