Variant report

Variant	rs4759416
Chromosome Location	chr12:123746357-123746358
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123746346-123746439	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123735701..123738592-chr12:123744837..123746422,2	MCF-7	breast:
2	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235423	TF binding region
ENSG00000269980	TF binding region
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10732573	0.82[EUR][1000 genomes]
rs10734901	0.82[EUR][1000 genomes]
rs10744149	0.84[AMR][1000 genomes]
rs10772995	0.83[AMR][1000 genomes]
rs10772998	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10773001	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10773002	0.83[EUR][1000 genomes]
rs10846478	0.84[AMR][1000 genomes]
rs10846486	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10846487	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10846491	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057192	0.85[AMR][1000 genomes]
rs11057204	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057206	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057210	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12817892	0.85[EUR][1000 genomes]
rs12818067	0.85[EUR][1000 genomes]
rs12824957	0.94[EUR][1000 genomes]
rs12829456	0.85[EUR][1000 genomes]
rs1402274	0.82[AMR][1000 genomes]
rs1402275	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533703	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1568427	0.80[EUR][1000 genomes]
rs1615694	0.84[AMR][1000 genomes]
rs1626899	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1630693	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1630905	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1716156	0.80[AMR][1000 genomes]
rs1716157	0.84[AMR][1000 genomes]
rs1716159	0.83[AMR][1000 genomes]
rs1716160	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1716164	0.83[AMR][1000 genomes]
rs1716170	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716171	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716172	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716173	0.83[AMR][1000 genomes]
rs1716175	0.83[AMR][1000 genomes]
rs1716176	0.82[AMR][1000 genomes]
rs1716177	0.82[AMR][1000 genomes]
rs1716182	0.82[AMR][1000 genomes]
rs1727290	0.82[AMR][1000 genomes]
rs1727300	0.83[AMR][1000 genomes]
rs1727306	0.83[AMR][1000 genomes]
rs1727320	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1727323	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1727325	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1727334	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790086	0.84[AMR][1000 genomes]
rs1790087	0.84[AMR][1000 genomes]
rs1790089	0.82[AMR][1000 genomes]
rs1790095	0.81[AMR][1000 genomes]
rs1790098	0.82[AMR][1000 genomes]
rs1790100	0.82[AMR][1000 genomes]
rs1790101	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1790102	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1790124	0.83[AMR][1000 genomes]
rs1790125	0.80[AMR][1000 genomes]
rs1790130	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1790131	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1879380	0.94[EUR][1000 genomes]
rs1969354	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1969355	0.80[EUR][1000 genomes]
rs1980251	0.82[EUR][1000 genomes]
rs1980252	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2049114	0.83[AMR][1000 genomes]
rs2337934	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2682430	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2682431	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2682434	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2851436	0.83[AMR][1000 genomes]
rs2851450	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2851451	0.84[AMR][1000 genomes]
rs2950537	0.82[AMR][1000 genomes]
rs3018098	0.82[AMR][1000 genomes]
rs34341465	0.85[EUR][1000 genomes]
rs4268544	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4372492	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4759371	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759409	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759415	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4759417	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58809476	0.85[EUR][1000 genomes]
rs6633	0.96[EUR][1000 genomes]
rs7313483	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7953929	0.90[EUR][1000 genomes]
rs941305	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs941306	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9795522	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4759416	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs4759416	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs4759416	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs4759416	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs4759416	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs4759416	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs4759416	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
4	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
5	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:123736000-123752200	Strong transcription	Dnd41	blood
8	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
10	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:123736400-123752600	Strong transcription	NHLF	lung
12	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
13	chr12:123737200-123752000	Strong transcription	A549	lung
14	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:123738000-123746600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:123738000-123748200	Strong transcription	Primary T cells from cord blood	blood
18	chr12:123738000-123749200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr12:123738000-123749200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:123738000-123749600	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:123738000-123749600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:123738000-123750400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:123738000-123751000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:123738000-123751200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:123738000-123751800	Strong transcription	Liver	Liver
26	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
27	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
29	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr12:123738200-123748400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:123738200-123751800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:123738200-123752000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr12:123738400-123748400	Strong transcription	NH-A	brain
35	chr12:123738600-123752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:123738800-123749800	Strong transcription	HSMMtube	muscle
37	chr12:123739000-123748600	Strong transcription	HSMM	muscle
38	chr12:123739000-123749400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:123739000-123751600	Strong transcription	Placenta	Placenta
40	chr12:123739200-123747000	Strong transcription	NHDF-Ad	bronchial
41	chr12:123739200-123748400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:123739200-123751800	Strong transcription	Adipose Nuclei	Adipose
43	chr12:123739200-123752600	Weak transcription	Psoas Muscle	Psoas
44	chr12:123739200-123753000	Weak transcription	Right Atrium	heart
45	chr12:123739200-123753200	Weak transcription	Fetal Heart	heart
46	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:123739400-123751800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:123739800-123747400	Strong transcription	Brain Anterior Caudate	brain
49	chr12:123739800-123748200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr12:123739800-123748400	Strong transcription	Brain Hippocampus Middle	brain

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