Variant report

Variant	rs417919
Chromosome Location	chr6:28779423-28779424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28778307..28780155-chr6:28804697..28807128,2	K562	blood:
2	chr6:28779162..28781130-chr6:28862892..28865549,2	K562	blood:
3	chr6:28692413..28694711-chr6:28778373..28780345,2	K562	blood:

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1233582	0.81[AMR][1000 genomes]
rs169682	1.00[ASN][1000 genomes]
rs185982	1.00[ASN][1000 genomes]
rs209181	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs209190	1.00[ASN][1000 genomes]
rs209192	1.00[ASN][1000 genomes]
rs209193	1.00[ASN][1000 genomes]
rs209199	1.00[ASN][1000 genomes]
rs2754761	0.85[ASN][1000 genomes]
rs2754762	1.00[ASN][1000 genomes]
rs2765220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765222	1.00[ASN][1000 genomes]
rs2765223	1.00[ASN][1000 genomes]
rs3131344	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398795	1.00[ASN][1000 genomes]
rs56030816	1.00[ASN][1000 genomes]
rs56308612	1.00[ASN][1000 genomes]
rs56374518	1.00[ASN][1000 genomes]
rs57491524	1.00[ASN][1000 genomes]
rs6938988	0.92[ASN][1000 genomes]
rs6939948	0.92[ASN][1000 genomes]
rs7739915	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9257182	0.81[AFR][1000 genomes]
rs9257190	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2621756	chr6:28762692-28779791	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2322180	chr6:28764675-28780578	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv970724	chr6:28778144-28784760	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs417919	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs417919	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs417919	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28778000-28779800	Flanking Active TSS	K562	blood
2	chr6:28778200-28781600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:28778800-28780000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:28778800-28780600	Bivalent Enhancer	HepG2	liver
5	chr6:28779000-28779800	Bivalent/Poised TSS	A549	lung
6	chr6:28779000-28780000	Weak transcription	HMEC	breast
7	chr6:28779200-28780200	Enhancers	Hela-S3	cervix
8	chr6:28779400-28779800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
9	chr6:28779400-28780000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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