Variant report

Variant	rs2273106
Chromosome Location	chr6:28499879-28499880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:28499436-28499908	K562	blood:	n/a	chr6:28499690-28499706
2	RAD21	chr6:28499438-28500023	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr6:28499465-28499913	HCT-116	colon:	n/a	n/a
4	CTCF	chr6:28499780-28499930	NHEK	skin:	n/a	n/a
5	CTCF	chr6:28499381-28499999	K562	blood:	n/a	chr6:28499690-28499706
6	RAD21	chr6:28499410-28499897	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr6:28499511-28499918	HCT-116	colon:	n/a	n/a
8	RAD21	chr6:28499492-28499883	SK-N-SH_RA	brain:	n/a	n/a
9	TEAD4	chr6:28499403-28499897	K562	blood:	n/a	n/a
10	CTCF	chr6:28499460-28499892	H1-hESC	embryonic stem cell:	n/a	chr6:28499690-28499706
11	RAD21	chr6:28499423-28499906	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr6:28499312-28499925	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28490306..28492074-chr6:28498929..28501971,3	K562	blood:
2	chr6:28499295..28501079-chr6:28547721..28550016,2	K562	blood:
3	chr6:28499347..28503956-chr6:28505758..28508912,7	K562	blood:
4	chr6:28498885..28501651-chr6:28502273..28504670,3	K562	blood:
5	chr6:28490306..28492074-chr6:28498929..28501092,2	K562	blood:
6	chr6:28494181..28496072-chr6:28498095..28502015,3	K562	blood:
7	chr6:28455084..28458229-chr6:28499553..28502958,3	K562	blood:

No data

Variant related genes	Relation type
GPX6	TF binding region
ENSG00000198704	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12660763	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12661782	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16894121	0.89[YRI][hapmap]
rs16894139	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2064424	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071966	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078035	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2078439	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2227228	0.83[CHD][hapmap]
rs28382604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859355	0.83[CHD][hapmap]
rs2859356	0.85[CHD][hapmap]
rs35327256	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35921765	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377514	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs380879	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs392230	0.82[AMR][1000 genomes]
rs448450	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4713166	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62402370	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456824	0.81[AMR][1000 genomes]
rs6921021	0.84[EUR][1000 genomes]
rs6933732	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72844230	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs769189	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468385	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs974334	0.83[CHD][hapmap]

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	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
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2273106	BTN2A3	cis	cerebellum	SCAN
rs2273106	HIST1H2BB	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28498600-28500000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr6:28498800-28500000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:28498800-28500000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:28498800-28500200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:28499200-28500200	Enhancers	K562	blood

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