Variant report

Variant	rs2516696
Chromosome Location	chr6:30235046-30235047
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30233853..30235858-chr6:30238091..30240138,2	K562	blood:
2	chr6:30227118..30230021-chr6:30233412..30236216,2	MCF-7	breast:
3	chr6:30233530..30235918-chr6:30253137..30255680,2	K562	blood:
4	chr6:30233837..30236152-chr6:30240056..30242630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243753	Chromatin interaction

Extended variants
information (count: 32 )
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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516708	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523740	0.98[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	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844766	0.98[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]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884061	chr6:30234627-30250450	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2516696	LOC401245	cis	multi-tissue	Pritchard
rs2516696	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
2	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
5	chr6:30228400-30239600	Weak transcription	HepG2	liver
6	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
8	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
12	chr6:30231600-30239600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:30232200-30235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:30232200-30235800	Weak transcription	Brain Anterior Caudate	brain
15	chr6:30232800-30235600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:30233000-30235200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:30233200-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:30233200-30235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:30233200-30243600	Weak transcription	HSMMtube	muscle
20	chr6:30233400-30235200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:30233400-30235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:30233400-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:30233400-30235600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:30233400-30236000	Weak transcription	Osteobl	bone
25	chr6:30233600-30235200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:30233800-30236200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:30233800-30241200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:30235000-30237400	Weak transcription	Primary B cells from cord blood	blood

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