Variant report

Variant	rs2765220
Chromosome Location	chr6:28769671-28769672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28769403..28772112-chr6:28910261..28912768,2	K562	blood:
2	chr6:28761012..28764011-chr6:28768099..28770643,2	K562	blood:
3	chr6:28768996..28771268-chr6:28774440..28778213,3	K562	blood:

Variant related genes	Relation type
ENSG00000265764	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 17 )

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	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[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]
rs2765222	1.00[ASN][1000 genomes]
rs2765223	1.00[ASN][1000 genomes]
rs3131344	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398795	1.00[ASN][1000 genomes]
rs417919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9257182	0.85[AFR][1000 genomes]
rs9257190	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257226	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3384463	chr6:28759027-28776259	Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2765220	HLA-H	cis	multi-tissue	Pritchard
rs2765220	ZKSCAN3	cis	cerebellum	SCAN
rs2765220	BTN3A2	cis	multi-tissue	Pritchard
rs2765220	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2765220	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2765220	HIST1H2BM	cis	cerebellum	SCAN
rs2765220	LRRC16A	cis	parietal	SCAN
rs2765220	HLA-A	cis	multi-tissue	Pritchard
rs2765220	ZFP57	cis	multi-tissue	Pritchard
rs2765220	ZSCAN23	cis	cerebellum	SCAN
rs2765220	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2765220	BTN3A3	cis	parietal	SCAN
rs2765220	ZNF192	cis	cerebellum	SCAN
rs2765220	ZNF323	cis	lymphoblastoid	seeQTL
rs2765220	ZNF323	cis	parietal	SCAN
rs2765220	ZSCAN23	cis	parietal	SCAN
rs2765220	HLA-G	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28763400-28770600	Weak transcription	HMEC	breast
2	chr6:28764600-28770400	Weak transcription	GM12878-XiMat	blood
3	chr6:28769600-28770200	Enhancers	K562	blood

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