Variant report

Variant	rs73231928
Chromosome Location	chr12:123724325-123724326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123448459..123450718-chr12:123723367..123726106,2	K562	blood:
2	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:
3	chr12:123459434..123462270-chr12:123721239..123724536,4	MCF-7	breast:
4	chr12:123721738..123724481-chr12:123725404..123728310,3	K562	blood:

Variant related genes	Relation type
ENSG00000111325	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000256028	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10744150	0.81[ASN][1000 genomes]
rs10744151	0.84[ASN][1000 genomes]
rs10772997	0.84[ASN][1000 genomes]
rs10772999	0.81[ASN][1000 genomes]
rs10773000	0.90[ASN][1000 genomes]
rs10846489	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057202	0.84[ASN][1000 genomes]
rs11057205	0.81[ASN][1000 genomes]
rs11057207	0.81[ASN][1000 genomes]
rs11057219	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11057224	0.84[ASN][1000 genomes]
rs1109559	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1109560	0.83[ASN][1000 genomes]
rs11610710	0.83[ASN][1000 genomes]
rs1568428	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1616484	0.90[AFR][1000 genomes]
rs1626703	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1716178	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1727286	0.83[ASN][1000 genomes]
rs1727301	0.82[ASN][1000 genomes]
rs1727331	0.83[ASN][1000 genomes]
rs1790088	0.83[ASN][1000 genomes]
rs1790096	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1790104	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1790129	0.87[ASN][1000 genomes]
rs1790134	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1879379	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2030401	0.84[ASN][1000 genomes]
rs2271976	0.84[ASN][1000 genomes]
rs2337630	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2337631	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682427	0.82[ASN][1000 genomes]
rs34841857	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4553407	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61519741	0.81[ASN][1000 genomes]
rs61953394	0.84[ASN][1000 genomes]
rs7137286	0.81[ASN][1000 genomes]
rs7139321	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304782	0.84[ASN][1000 genomes]
rs7312955	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73231928	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs73231928	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
4	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
5	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
6	chr12:123719000-123724400	Weak transcription	HSMM	muscle
7	chr12:123719000-123725000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
11	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:123719200-123726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:123719200-123735200	Weak transcription	Ovary	ovary
21	chr12:123719400-123726600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:123719600-123726400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
24	chr12:123719600-123738400	Weak transcription	NH-A	brain
25	chr12:123719800-123726200	Weak transcription	Fetal Lung	lung
26	chr12:123719800-123726400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:123719800-123726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:123719800-123726800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:123719800-123726800	Weak transcription	NHDF-Ad	bronchial
30	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
31	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
33	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
34	chr12:123720000-123726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:123720000-123726200	Weak transcription	Psoas Muscle	Psoas
36	chr12:123720000-123726400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:123720000-123726400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:123720000-123726400	Weak transcription	Brain Angular Gyrus	brain
39	chr12:123720000-123726400	Weak transcription	Brain Anterior Caudate	brain
40	chr12:123720000-123726400	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:123720000-123726400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:123720000-123726400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:123720000-123726600	Weak transcription	HUVEC	blood vessel
44	chr12:123720000-123726800	Weak transcription	Left Ventricle	heart
45	chr12:123720000-123726800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:123720000-123732800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:123720000-123736000	Weak transcription	Gastric	stomach
48	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
49	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
50	chr12:123720600-123733000	Weak transcription	Fetal Brain Female	brain

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