Variant report

Variant	rs2028654
Chromosome Location	chr18:9343199-9343200
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9336509..9338927-chr18:9340961..9343799,3	MCF-7	breast:
2	chr18:9341334..9344223-chr18:9346131..9348599,3	K562	blood:
3	chr18:9340188..9343465-chr18:9348198..9351068,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10853376	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081473	0.91[ASN][1000 genomes]
rs11081474	0.85[ASN][1000 genomes]
rs11873989	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11875585	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11875640	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11876171	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11876202	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12604438	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12956692	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12962014	0.92[ASN][1000 genomes]
rs1443594	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443595	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443599	0.91[ASN][1000 genomes]
rs2028655	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120317	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3786173	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3859293	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4567794	0.92[ASN][1000 genomes]
rs4798794	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57524426	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6506652	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506653	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506654	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7233925	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7234762	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7237850	0.80[ASN][1000 genomes]
rs8085920	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8087892	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8095060	0.89[ASN][1000 genomes]
rs8096911	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8096988	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8097654	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925100	0.91[ASN][1000 genomes]
rs9635818	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635873	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9956536	0.91[ASN][1000 genomes]
rs9957701	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9967388	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028654	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 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	chr18:9335600-9343800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
6	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr18:9335800-9343600	Weak transcription	Primary B cells from cord blood	blood
8	chr18:9335800-9343600	Weak transcription	Primary T cells from cord blood	blood
9	chr18:9335800-9343800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:9335800-9344000	Weak transcription	Esophagus	oesophagus
11	chr18:9335800-9345200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:9335800-9348000	Weak transcription	Psoas Muscle	Psoas
13	chr18:9335800-9348200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr18:9335800-9348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr18:9335800-9348400	Weak transcription	Thymus	Thymus
16	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
19	chr18:9335800-9367600	Weak transcription	Lung	lung
20	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
21	chr18:9336000-9343200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr18:9336000-9346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr18:9336000-9348000	Weak transcription	Hela-S3	cervix
24	chr18:9336000-9348400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr18:9336000-9348400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr18:9336000-9348600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
29	chr18:9336200-9343600	Weak transcription	A549	lung
30	chr18:9336200-9346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr18:9336200-9347600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr18:9336200-9348000	Weak transcription	HepG2	liver
33	chr18:9336200-9348200	Weak transcription	HMEC	breast
34	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
35	chr18:9336400-9349400	Weak transcription	Fetal Intestine Small	intestine
36	chr18:9337200-9343400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:9337200-9343400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:9337200-9346400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:9337200-9346800	Strong transcription	Fetal Muscle Leg	muscle
40	chr18:9337400-9345000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:9337600-9347600	Strong transcription	HSMM	muscle
42	chr18:9337800-9345600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:9338000-9343800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr18:9338000-9345400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:9338200-9345800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:9338200-9348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr18:9338200-9354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr18:9338400-9343400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr18:9338400-9343600	Weak transcription	Fetal Heart	heart
50	chr18:9338400-9346600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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