Variant report

Variant	rs12829456
Chromosome Location	chr12:123725395-123725396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123448459..123450718-chr12:123723367..123726106,2	K562	blood:
2	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1047158	0.82[EUR][1000 genomes]
rs1051431	0.83[EUR][1000 genomes]
rs10744151	0.81[EUR][1000 genomes]
rs10772993	0.84[EUR][1000 genomes]
rs10772995	0.84[EUR][1000 genomes]
rs10772998	0.96[EUR][1000 genomes]
rs10772999	0.81[EUR][1000 genomes]
rs10773001	0.88[EUR][1000 genomes]
rs10846478	0.84[EUR][1000 genomes]
rs10846486	0.87[EUR][1000 genomes]
rs10846487	0.95[EUR][1000 genomes]
rs10846491	0.85[EUR][1000 genomes]
rs11057192	0.88[EUR][1000 genomes]
rs11057202	0.81[EUR][1000 genomes]
rs11057204	0.97[EUR][1000 genomes]
rs11057205	0.81[EUR][1000 genomes]
rs11057206	0.96[EUR][1000 genomes]
rs11057207	0.81[EUR][1000 genomes]
rs11057210	0.95[EUR][1000 genomes]
rs1106240	0.83[EUR][1000 genomes]
rs1106241	0.81[EUR][1000 genomes]
rs12817892	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12818067	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12821431	0.81[AFR][1000 genomes]
rs12824957	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1402274	0.86[EUR][1000 genomes]
rs1402275	0.85[EUR][1000 genomes]
rs1533703	0.89[EUR][1000 genomes]
rs1569068	0.81[EUR][1000 genomes]
rs1615694	0.84[EUR][1000 genomes]
rs1616131	0.80[EUR][1000 genomes]
rs1616181	0.80[EUR][1000 genomes]
rs1617434	0.85[EUR][1000 genomes]
rs1618679	0.80[EUR][1000 genomes]
rs1621194	0.83[EUR][1000 genomes]
rs1626899	0.89[EUR][1000 genomes]
rs1627724	0.82[EUR][1000 genomes]
rs1630693	0.87[EUR][1000 genomes]
rs1630905	0.87[EUR][1000 genomes]
rs1716156	0.81[EUR][1000 genomes]
rs1716157	0.84[EUR][1000 genomes]
rs1716159	0.84[EUR][1000 genomes]
rs1716160	0.88[EUR][1000 genomes]
rs1716164	0.82[EUR][1000 genomes]
rs1716165	0.83[EUR][1000 genomes]
rs1716167	0.83[EUR][1000 genomes]
rs1716168	0.82[EUR][1000 genomes]
rs1716169	0.84[EUR][1000 genomes]
rs1716170	0.96[EUR][1000 genomes]
rs1716171	0.96[EUR][1000 genomes]
rs1716172	0.94[EUR][1000 genomes]
rs1716173	0.81[EUR][1000 genomes]
rs1716175	0.84[EUR][1000 genomes]
rs1716176	0.86[EUR][1000 genomes]
rs1716177	0.86[EUR][1000 genomes]
rs1716182	0.83[EUR][1000 genomes]
rs1727290	0.86[EUR][1000 genomes]
rs1727294	0.80[EUR][1000 genomes]
rs1727296	0.83[EUR][1000 genomes]
rs1727300	0.82[EUR][1000 genomes]
rs1727306	0.84[EUR][1000 genomes]
rs1727309	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1727310	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1727313	0.82[EUR][1000 genomes]
rs1727314	0.81[EUR][1000 genomes]
rs1727315	0.82[EUR][1000 genomes]
rs1727316	0.80[EUR][1000 genomes]
rs1727317	0.82[EUR][1000 genomes]
rs1727320	0.88[EUR][1000 genomes]
rs1727322	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1727323	0.88[EUR][1000 genomes]
rs1727324	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1727325	0.88[EUR][1000 genomes]
rs1727332	0.82[EUR][1000 genomes]
rs1727334	0.96[EUR][1000 genomes]
rs1790086	0.84[EUR][1000 genomes]
rs1790087	0.84[EUR][1000 genomes]
rs1790089	0.86[EUR][1000 genomes]
rs1790090	0.82[EUR][1000 genomes]
rs1790095	0.86[EUR][1000 genomes]
rs1790098	0.86[EUR][1000 genomes]
rs1790100	0.86[EUR][1000 genomes]
rs1790101	0.87[EUR][1000 genomes]
rs1790102	0.86[EUR][1000 genomes]
rs1790108	0.82[EUR][1000 genomes]
rs1790109	0.82[EUR][1000 genomes]
rs1790116	0.80[EUR][1000 genomes]
rs1790123	0.86[EUR][1000 genomes]
rs1790124	0.82[EUR][1000 genomes]
rs1790130	0.86[EUR][1000 genomes]
rs1790131	0.87[EUR][1000 genomes]
rs1879380	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1969354	0.89[EUR][1000 genomes]
rs1980252	0.87[EUR][1000 genomes]
rs2049114	0.84[EUR][1000 genomes]
rs2337934	0.87[EUR][1000 genomes]
rs2682429	0.82[EUR][1000 genomes]
rs2682430	0.86[EUR][1000 genomes]
rs2682431	0.88[EUR][1000 genomes]
rs2682433	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2682434	0.88[EUR][1000 genomes]
rs2695476	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2695478	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2695479	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2695480	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2695481	0.82[EUR][1000 genomes]
rs2695482	0.81[EUR][1000 genomes]
rs2851435	0.92[EUR][1000 genomes]
rs2851436	0.82[EUR][1000 genomes]
rs2851438	0.82[EUR][1000 genomes]
rs2851450	0.88[EUR][1000 genomes]
rs2851451	0.87[EUR][1000 genomes]
rs2947099	0.83[EUR][1000 genomes]
rs2950537	0.82[EUR][1000 genomes]
rs3018098	0.86[EUR][1000 genomes]
rs34341465	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4268544	0.88[EUR][1000 genomes]
rs4372492	0.88[EUR][1000 genomes]
rs4759371	0.89[EUR][1000 genomes]
rs4759409	0.94[EUR][1000 genomes]
rs4759415	0.87[EUR][1000 genomes]
rs4759416	0.85[EUR][1000 genomes]
rs4759417	0.86[EUR][1000 genomes]
rs58809476	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6633	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7137286	0.81[EUR][1000 genomes]
rs7313483	0.95[EUR][1000 genomes]
rs7953929	0.84[EUR][1000 genomes]
rs884548	0.82[EUR][1000 genomes]
rs941305	0.96[EUR][1000 genomes]
rs941306	0.96[EUR][1000 genomes]
rs949142	0.82[EUR][1000 genomes]
rs9795522	0.96[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12829456	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs12829456	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12829456	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12829456	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs12829456	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs12829456	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs12829456	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs12829456	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12829456	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12829456	LOC283378	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
9	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:123719200-123726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:123719200-123735200	Weak transcription	Ovary	ovary
19	chr12:123719400-123726600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:123719600-123726400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
22	chr12:123719600-123738400	Weak transcription	NH-A	brain
23	chr12:123719800-123726200	Weak transcription	Fetal Lung	lung
24	chr12:123719800-123726400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:123719800-123726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:123719800-123726800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:123719800-123726800	Weak transcription	NHDF-Ad	bronchial
28	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
29	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
31	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
32	chr12:123720000-123726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:123720000-123726200	Weak transcription	Psoas Muscle	Psoas
34	chr12:123720000-123726400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:123720000-123726400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:123720000-123726400	Weak transcription	Brain Angular Gyrus	brain
37	chr12:123720000-123726400	Weak transcription	Brain Anterior Caudate	brain
38	chr12:123720000-123726400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:123720000-123726400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:123720000-123726400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:123720000-123726600	Weak transcription	HUVEC	blood vessel
42	chr12:123720000-123726800	Weak transcription	Left Ventricle	heart
43	chr12:123720000-123726800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:123720000-123732800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:123720000-123736000	Weak transcription	Gastric	stomach
46	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
47	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
48	chr12:123720600-123733000	Weak transcription	Fetal Brain Female	brain
49	chr12:123720800-123727400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:123721000-123733800	Weak transcription	Lung	lung

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