Variant report

Variant	rs209165
Chromosome Location	chr6:28829486-28829487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28827198..28830005-chr6:28973058..28974944,2	K562	blood:
2	chr6:28806019..28808869-chr6:28827811..28829720,2	K562	blood:
3	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
4	chr6:28804491..28806748-chr6:28829481..28831000,2	MCF-7	breast:
5	chr6:28806762..28809202-chr6:28828058..28830893,2	MCF-7	breast:
6	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-3	chr6:28827402-28829792	ENSG00000225595
2	lnc-TRIM27-3	chr6:28828927-28829792	ENSG00000225595.2
3	lnc-TRIM27-3	chr6:28827402-28829792	NONHSAT108488

No data

Variant related genes	Relation type
ENSG00000197935	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000233366	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1061625	0.84[ASN][1000 genomes]
rs172326	0.95[ASN][1000 genomes]
rs1794588	0.85[ASN][1000 genomes]
rs184094	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013652	0.88[ASN][1000 genomes]
rs209127	0.86[ASN][1000 genomes]
rs209140	0.93[ASN][1000 genomes]
rs209147	0.98[ASN][1000 genomes]
rs209151	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209172	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209177	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209180	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2097424	0.87[ASN][1000 genomes]
rs2148007	0.89[ASN][1000 genomes]
rs2269553	0.84[ASN][1000 genomes]
rs28381661	0.83[ASN][1000 genomes]
rs28381663	0.81[ASN][1000 genomes]
rs28743260	0.83[ASN][1000 genomes]
rs2894066	0.84[ASN][1000 genomes]
rs3131067	0.81[ASN][1000 genomes]
rs3132377	0.84[ASN][1000 genomes]
rs3132380	0.81[ASN][1000 genomes]
rs3135314	0.92[ASN][1000 genomes]
rs413972	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422331	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs429369	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484511	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6909419	0.81[ASN][1000 genomes]
rs743847	0.92[ASN][1000 genomes]
rs7750338	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7763940	0.83[ASN][1000 genomes]
rs7769221	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7776376	0.83[ASN][1000 genomes]
rs876737	0.81[ASN][1000 genomes]
rs9257269	0.89[ASN][1000 genomes]
rs9257270	0.89[ASN][1000 genomes]
rs9257274	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9257280	0.91[ASN][1000 genomes]
rs9257281	0.92[ASN][1000 genomes]
rs9257328	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs929042	0.84[ASN][1000 genomes]
rs9368576	0.83[ASN][1000 genomes]
rs9378149	0.83[ASN][1000 genomes]
rs9393932	0.83[ASN][1000 genomes]
rs9393933	0.83[ASN][1000 genomes]
rs9404976	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	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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	esv3403240	chr6:28808022-28832799	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs209165	ZKSCAN3	cis	cerebellum	SCAN
rs209165	HIST1H2AE	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28825400-28830200	Weak transcription	K562	blood
2	chr6:28828200-28829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:28828400-28830800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:28828800-28829800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:28829000-28830000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:28829400-28829600	Enhancers	HMEC	breast
7	chr6:28829400-28830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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