Variant report

Variant	rs4268544
Chromosome Location	chr12:123734774-123734775
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
2	chr12:123733760..123735468-chr12:123740461..123742402,2	K562	blood:
3	chr12:123733810..123737382-chr12:123754694..123758405,4	MCF-7	breast:
4	chr12:123715816..123718191-chr12:123733182..123735641,3	K562	blood:
5	chr12:123728345..123730190-chr12:123734058..123735826,2	MCF-7	breast:
6	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235423	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1047158	0.82[AMR][1000 genomes]
rs1051431	0.82[AMR][1000 genomes]
rs10744149	0.89[AMR][1000 genomes]
rs10772995	0.88[AMR][1000 genomes]
rs10772996	0.81[AMR][1000 genomes]
rs10772998	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10773001	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10846478	0.89[AMR][1000 genomes]
rs10846486	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10846487	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10846491	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11057192	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11057204	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11057206	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057207	0.80[EUR][1000 genomes]
rs11057209	0.81[EUR][1000 genomes]
rs11057210	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12817892	0.88[EUR][1000 genomes]
rs12818067	0.88[EUR][1000 genomes]
rs12824957	0.82[EUR][1000 genomes]
rs12829456	0.88[EUR][1000 genomes]
rs1402274	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1402275	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1533703	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1609520	0.83[EUR][1000 genomes]
rs1615694	0.89[AMR][1000 genomes]
rs1621194	0.82[AMR][1000 genomes]
rs1626899	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1630693	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1630905	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716156	0.85[AMR][1000 genomes]
rs1716157	0.89[AMR][1000 genomes]
rs1716158	0.81[AMR][1000 genomes]
rs1716159	0.88[AMR][1000 genomes]
rs1716160	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716164	0.88[AMR][1000 genomes]
rs1716165	0.82[AMR][1000 genomes]
rs1716167	0.82[AMR][1000 genomes]
rs1716168	0.82[AMR][1000 genomes]
rs1716170	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716171	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716172	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716173	0.88[AMR][1000 genomes]
rs1716175	0.88[AMR][1000 genomes]
rs1716176	0.87[AMR][1000 genomes]
rs1716177	0.87[AMR][1000 genomes]
rs1716182	0.87[AMR][1000 genomes]
rs1727290	0.87[AMR][1000 genomes]
rs1727296	0.82[AMR][1000 genomes]
rs1727300	0.88[AMR][1000 genomes]
rs1727306	0.88[AMR][1000 genomes]
rs1727314	0.82[AMR][1000 genomes]
rs1727320	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1727323	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1727325	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1727334	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790086	0.89[AMR][1000 genomes]
rs1790087	0.89[AMR][1000 genomes]
rs1790089	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790095	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790098	0.87[AMR][1000 genomes]
rs1790100	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790101	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790102	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790124	0.88[AMR][1000 genomes]
rs1790125	0.85[AMR][1000 genomes]
rs1790130	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790131	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879380	0.85[EUR][1000 genomes]
rs1969354	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980252	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2049114	0.88[AMR][1000 genomes]
rs2337934	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682429	0.82[AMR][1000 genomes]
rs2682430	0.93[AMR][1000 genomes]
rs2682431	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682434	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2695481	0.82[AMR][1000 genomes]
rs2851435	0.80[EUR][1000 genomes]
rs2851436	0.88[AMR][1000 genomes]
rs2851438	0.82[AMR][1000 genomes]
rs2851450	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851451	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2950537	0.87[AMR][1000 genomes]
rs3018098	0.87[AMR][1000 genomes]
rs34341465	0.88[EUR][1000 genomes]
rs4372492	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4759371	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759409	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759415	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4759416	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4759417	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58809476	0.88[EUR][1000 genomes]
rs6633	0.83[EUR][1000 genomes]
rs7313483	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs941305	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs941306	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9795522	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[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
rs4268544	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs4268544	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs4268544	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs4268544	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs4268544	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs4268544	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs4268544	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
2	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:123719200-123735200	Weak transcription	Ovary	ovary
4	chr12:123719600-123738400	Weak transcription	NH-A	brain
5	chr12:123720000-123736000	Weak transcription	Gastric	stomach
6	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
7	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
8	chr12:123721600-123735200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:123723400-123735000	Weak transcription	Stomach Mucosa	stomach
10	chr12:123724600-123735200	Weak transcription	Placenta	Placenta
11	chr12:123725200-123738000	Weak transcription	HSMM	muscle
12	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:123726600-123735200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:123727000-123735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:123727200-123735000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:123727200-123735000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:123727200-123735000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:123727200-123735200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:123727400-123734800	Weak transcription	Hela-S3	cervix
20	chr12:123727400-123735000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:123727400-123735000	Weak transcription	Brain Anterior Caudate	brain
22	chr12:123727400-123735000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:123727400-123735000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:123727400-123735200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:123727400-123735200	Weak transcription	Brain Angular Gyrus	brain
26	chr12:123727400-123735200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:123727400-123735200	Weak transcription	Fetal Brain Male	brain
28	chr12:123727400-123735400	Weak transcription	Right Atrium	heart
29	chr12:123727400-123736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:123727400-123738000	Weak transcription	NHDF-Ad	bronchial
31	chr12:123727400-123738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:123727600-123735000	Weak transcription	Left Ventricle	heart
33	chr12:123727600-123735000	Weak transcription	HepG2	liver
34	chr12:123727600-123735200	Weak transcription	Adipose Nuclei	Adipose
35	chr12:123727600-123735200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:123727600-123735200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:123727600-123736400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:123727600-123738000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:123727600-123738000	Weak transcription	HUVEC	blood vessel
40	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:123727800-123735400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:123727800-123738200	Weak transcription	Fetal Heart	heart
43	chr12:123728000-123735000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:123728400-123735200	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:123729400-123735000	Strong transcription	Fetal Thymus	thymus
46	chr12:123731800-123735600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr12:123732000-123738200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:123732200-123735000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:123732200-123735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:123732800-123735000	Strong transcription	Primary B cells from peripheral blood	blood

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