Variant report

Variant	rs2516677
Chromosome Location	chr6:30424623-30424624
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30422351..30425241-chr6:30448232..30450888,2	MCF-7	breast:
2	chr6:30424289..30426126-chr6:30523378..30525417,2	K562	blood:
3	chr6:30423219..30426193-chr6:30426415..30429085,2	K562	blood:

Variant related genes	Relation type
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1077501	0.85[ASN][1000 genomes]
rs1150770	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1264511	0.84[ASN][1000 genomes]
rs1264513	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1264516	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1264542	0.81[ASN][1000 genomes]
rs1268444	0.84[ASN][1000 genomes]
rs1268445	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2105961	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2187974	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187975	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516674	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516678	0.84[ASN][1000 genomes]
rs2524175	0.84[ASN][1000 genomes]
rs2524176	0.84[ASN][1000 genomes]
rs2524178	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2524179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2524180	0.86[ASN][1000 genomes]
rs2524182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524183	0.86[ASN][1000 genomes]
rs2524186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2524188	0.86[ASN][1000 genomes]
rs2524189	0.86[ASN][1000 genomes]
rs2524197	0.86[ASN][1000 genomes]
rs2524198	0.86[ASN][1000 genomes]
rs2524200	0.86[ASN][1000 genomes]
rs2524201	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2844729	0.86[ASN][1000 genomes]
rs2844730	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3094716	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3131114	0.86[ASN][1000 genomes]
rs915666	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs928821	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs978009	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601478	chr6:30383768-30438226	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3336846	chr6:30420111-30432946	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2516677	HLA-DQA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30419200-30428600	Weak transcription	Pancreas	Pancrea

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