Variant report

Variant	rs2516708
Chromosome Location	chr6:30228721-30228722
allele	C/T
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
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1075105	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12055553	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12192505	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1264617	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1264618	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1264619	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2187979	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523740	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261947	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844759	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2844760	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2844762	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711213	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6900042	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6906180	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6912771	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6913293	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6924282	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6924453	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6931387	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9295842	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9357098	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9368635	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9380167	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9380172	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2516708	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs2516708	HLA-A	cis	lymphoblastoid	GTEx

Chromatin state (count:73 , 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	chr6:30226800-30228800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:30227200-30228800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:30227200-30228800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:30227200-30228800	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr6:30227200-30228800	Active TSS	Osteobl	bone
7	chr6:30227800-30228800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr6:30228000-30228800	Flanking Active TSS	Right Ventricle	heart
9	chr6:30228000-30229800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:30228200-30228800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr6:30228200-30228800	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
12	chr6:30228200-30228800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:30228200-30228800	Enhancers	Lung	lung
14	chr6:30228200-30229400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:30228200-30231200	Weak transcription	Ovary	ovary
16	chr6:30228200-30232000	Weak transcription	HSMMtube	muscle
17	chr6:30228200-30234200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
19	chr6:30228400-30228800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:30228400-30228800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:30228400-30228800	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:30228400-30228800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:30228400-30228800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr6:30228400-30229000	Enhancers	Primary B cells from cord blood	blood
25	chr6:30228400-30229000	Active TSS	Spleen	Spleen
26	chr6:30228400-30229000	Weak transcription	NHLF	lung
27	chr6:30228400-30229200	Enhancers	Brain Angular Gyrus	brain
28	chr6:30228400-30229200	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:30228400-30229200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:30228400-30229600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:30228400-30230000	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr6:30228400-30230000	Weak transcription	Colonic Mucosa	Colon
33	chr6:30228400-30230400	Weak transcription	Small Intestine	intestine
34	chr6:30228400-30230800	Weak transcription	NH-A	brain
35	chr6:30228400-30231400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:30228400-30231400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30228400-30231400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:30228400-30231400	Weak transcription	HMEC	breast
39	chr6:30228400-30231400	Weak transcription	NHDF-Ad	bronchial
40	chr6:30228400-30231600	Weak transcription	HSMM	muscle
41	chr6:30228400-30231800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:30228400-30232400	Weak transcription	Brain Germinal Matrix	brain
43	chr6:30228400-30232400	Weak transcription	Gastric	stomach
44	chr6:30228400-30232800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
48	chr6:30228400-30239600	Weak transcription	HepG2	liver
49	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:30228600-30228800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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