Variant report

Variant	rs12457923
Chromosome Location	chr18:9339571-9339572
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	chr18:9339033..9342733-chr18:9344110..9350817,6	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11875065	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12456325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12458365	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16954989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16954996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34741369	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56349417	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57333366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57456386	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62087465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62087466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62087468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087472	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62087494	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7229150	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7233757	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7243117	0.80[EUR][1000 genomes]
rs8088103	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8093378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8093683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9676006	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9748497	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9748605	0.93[AMR][1000 genomes];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12457923	TWSG1	cis	Muscle Skeletal	GTEx
rs12457923	TWSG1	cis	Artery Tibial	GTEx
rs12457923	TWSG1	Cis_1M	lymphoblastoid	RTeQTL
rs12457923	TWSG1	cis	Thyroid	GTEx
rs12457923	TWSG1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9335400-9340400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:9335400-9347800	Weak transcription	Small Intestine	intestine
3	chr18:9335400-9369400	Weak transcription	Pancreas	Pancrea
4	chr18:9335400-9371400	Weak transcription	Gastric	stomach
5	chr18:9335600-9343800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
7	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr18:9335800-9340600	Weak transcription	Liver	Liver
9	chr18:9335800-9341400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr18:9335800-9341400	Weak transcription	Spleen	Spleen
11	chr18:9335800-9341800	Weak transcription	Right Atrium	heart
12	chr18:9335800-9342600	Weak transcription	Right Ventricle	heart
13	chr18:9335800-9343600	Weak transcription	Primary B cells from cord blood	blood
14	chr18:9335800-9343600	Weak transcription	Primary T cells from cord blood	blood
15	chr18:9335800-9343800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:9335800-9344000	Weak transcription	Esophagus	oesophagus
17	chr18:9335800-9345200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr18:9335800-9348000	Weak transcription	Psoas Muscle	Psoas
19	chr18:9335800-9348200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:9335800-9348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:9335800-9348400	Weak transcription	Thymus	Thymus
22	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
25	chr18:9335800-9367600	Weak transcription	Lung	lung
26	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
27	chr18:9336000-9343200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr18:9336000-9346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr18:9336000-9348000	Weak transcription	Hela-S3	cervix
30	chr18:9336000-9348400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr18:9336000-9348400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr18:9336000-9348600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
35	chr18:9336200-9342200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:9336200-9343600	Weak transcription	A549	lung
37	chr18:9336200-9346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:9336200-9347600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr18:9336200-9348000	Weak transcription	HepG2	liver
40	chr18:9336200-9348200	Weak transcription	HMEC	breast
41	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
42	chr18:9336400-9340600	Weak transcription	Fetal Brain Male	brain
43	chr18:9336400-9349400	Weak transcription	Fetal Intestine Small	intestine
44	chr18:9337200-9341000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr18:9337200-9341200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr18:9337200-9342200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr18:9337200-9343400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:9337200-9343400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:9337200-9346400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:9337200-9346800	Strong transcription	Fetal Muscle Leg	muscle

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