Variant report

Variant	rs2523748
Chromosome Location	chr6:30228881-30228882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30225449..30228967-chr6:30292795..30296377,4	K562	blood:
2	chr6:30226682..30228906-chr6:30311932..30314057,2	MCF-7	breast:
3	chr6:30177177..30179717-chr6:30228563..30230650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231074	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000270604	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1045251	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060065	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264616	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1473102	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023476	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2023477	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2023478	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2057727	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074474	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097773	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2394780	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508026	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2516697	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516699	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516700	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516702	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516704	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516705	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516706	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2516707	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516710	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516713	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516718	0.80[AFR][1000 genomes]
rs2523737	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2523744	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523745	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523746	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523747	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523750	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs261943	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs261948	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs261949	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28360021	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28360023	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844752	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844761	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844763	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844765	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778624	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912239	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6912495	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7452694	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7767817	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295843	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380168	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380174	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394001	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9394003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs962899	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs974963	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2523748	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs2523748	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30226600-30229000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:30228000-30229800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:30228200-30229400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:30228200-30231200	Weak transcription	Ovary	ovary
5	chr6:30228200-30232000	Weak transcription	HSMMtube	muscle
6	chr6:30228200-30234200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
8	chr6:30228400-30229000	Enhancers	Primary B cells from cord blood	blood
9	chr6:30228400-30229000	Active TSS	Spleen	Spleen
10	chr6:30228400-30229000	Weak transcription	NHLF	lung
11	chr6:30228400-30229200	Enhancers	Brain Angular Gyrus	brain
12	chr6:30228400-30229200	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:30228400-30229200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr6:30228400-30229600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:30228400-30230000	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr6:30228400-30230000	Weak transcription	Colonic Mucosa	Colon
17	chr6:30228400-30230400	Weak transcription	Small Intestine	intestine
18	chr6:30228400-30230800	Weak transcription	NH-A	brain
19	chr6:30228400-30231400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30228400-30231400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:30228400-30231400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:30228400-30231400	Weak transcription	HMEC	breast
23	chr6:30228400-30231400	Weak transcription	NHDF-Ad	bronchial
24	chr6:30228400-30231600	Weak transcription	HSMM	muscle
25	chr6:30228400-30231800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:30228400-30232400	Weak transcription	Brain Germinal Matrix	brain
27	chr6:30228400-30232400	Weak transcription	Gastric	stomach
28	chr6:30228400-30232800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
32	chr6:30228400-30239600	Weak transcription	HepG2	liver
33	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:30228600-30229000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
35	chr6:30228600-30229000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr6:30228600-30229000	Active TSS	Stomach Smooth Muscle	stomach
37	chr6:30228600-30229000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
38	chr6:30228600-30229200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:30228600-30229200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:30228600-30229400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:30228600-30230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:30228600-30230800	Weak transcription	Brain Anterior Caudate	brain
43	chr6:30228600-30230800	Weak transcription	Pancreas	Pancrea
44	chr6:30228600-30232200	Weak transcription	Fetal Brain Male	brain
45	chr6:30228600-30233000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:30228600-30233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:30228600-30233200	Weak transcription	Thymus	Thymus
48	chr6:30228600-30233800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:30228600-30234400	Weak transcription	Fetal Brain Female	brain
50	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain

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