Variant report

Variant	rs35546888
Chromosome Location	chr6:28558890-28558891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28558273..28560922-chr6:28562703..28565525,2	K562	blood:
2	chr6:28558273..28560573-chr6:28562047..28564203,2	K562	blood:
3	chr6:28556555..28559076-chr6:28582763..28585041,2	K562	blood:
4	chr6:28558077..28560293-chr6:28570490..28573084,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX5-1	chr6:28557006-28559524	XLOC_005223

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11963067	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965972	0.91[ASN][1000 genomes]
rs11966966	0.82[ASN][1000 genomes]
rs11967609	0.82[ASN][1000 genomes]
rs11970339	0.83[ASN][1000 genomes]
rs11970409	0.82[ASN][1000 genomes]
rs13217047	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13220637	0.83[ASN][1000 genomes]
rs16894194	0.83[ASN][1000 genomes]
rs16894197	0.83[ASN][1000 genomes]
rs16901848	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17336532	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1884936	0.83[ASN][1000 genomes]
rs1884937	0.83[ASN][1000 genomes]
rs2394120	0.81[ASN][1000 genomes]
rs2394121	0.83[ASN][1000 genomes]
rs2893966	0.83[ASN][1000 genomes]
rs34020953	0.83[ASN][1000 genomes]
rs34177106	0.83[ASN][1000 genomes]
rs34388845	0.93[ASN][1000 genomes]
rs34556183	0.91[ASN][1000 genomes]
rs35257859	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35466817	0.83[ASN][1000 genomes]
rs36069097	0.86[ASN][1000 genomes]
rs36103239	0.91[ASN][1000 genomes]
rs4121091	0.83[ASN][1000 genomes]
rs41270599	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56389860	0.83[ASN][1000 genomes]
rs61229539	0.83[ASN][1000 genomes]
rs6923110	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941188	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742957	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767008	0.83[ASN][1000 genomes]
rs7775683	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35546888	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35546888	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs35546888	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28557400-28559000	Enhancers	Pancreas	Pancrea
3	chr6:28558000-28565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28558800-28559600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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