Variant report

Variant	rs2396502
Chromosome Location	chr6:45357699-45357700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45344406..45349479-chr6:45352255..45358580,11	MCF-7	breast:
2	chr6:45355709..45357704-chr6:45363797..45365580,2	K562	blood:
3	chr6:45357171..45359418-chr6:45385191..45386849,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10948222	0.84[EUR][1000 genomes]
rs10948231	0.87[ASN][1000 genomes]
rs12199720	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12205312	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12209727	0.98[ASN][1000 genomes]
rs12525950	0.87[ASN][1000 genomes]
rs1321081	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17288334	0.98[ASN][1000 genomes]
rs35565233	0.87[ASN][1000 genomes]
rs3749863	0.95[EUR][1000 genomes]
rs3923353	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4373351	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4446571	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4510673	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62400336	0.98[ASN][1000 genomes]
rs6458441	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6934594	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6935398	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs717987	0.87[ASN][1000 genomes]
rs7451423	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7740083	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7770401	0.87[EUR][1000 genomes]
rs9296453	0.81[EUR][1000 genomes]
rs9296457	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9357480	0.80[EUR][1000 genomes]
rs9357484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9369552	0.81[EUR][1000 genomes]
rs9369558	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9381383	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9395086	0.83[EUR][1000 genomes]
rs9395095	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9463081	0.82[EUR][1000 genomes]
rs9463083	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9472460	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2396502	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45354200-45358600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr6:45354400-45358200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:45356200-45357800	Weak transcription	HSMMtube	muscle
4	chr6:45356200-45358400	Enhancers	Osteobl	bone
5	chr6:45356800-45382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:45357400-45357800	Enhancers	Placenta	Placenta
7	chr6:45357400-45358000	Weak transcription	NHDF-Ad	bronchial

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