Variant report

Variant	rs4559087
Chromosome Location	chr6:27267008-27267009
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27265877..27267509-chr6:27513280..27515497,2	K562	blood:
2	chr6:27266213..27267894-chr6:27269235..27271066,2	K562	blood:
3	chr6:27113560..27116380-chr6:27265078..27267189,2	K562	blood:
4	chr6:27172666..27175265-chr6:27265465..27267285,2	K562	blood:
5	chr6:27112367..27116319-chr6:27264620..27267784,3	K562	blood:
6	chr6:27155262..27157566-chr6:27266020..27269001,2	K562	blood:
7	chr6:27197041..27202373-chr6:27261458..27267425,7	K562	blood:
8	chr6:27260999..27263500-chr6:27265988..27267831,3	K562	blood:
9	chr6:27263999..27267440-chr6:27299677..27302604,5	K562	blood:
10	chr6:27097573..27099800-chr6:27264464..27267307,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10946904	0.89[CHB][hapmap]
rs2092114	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2295603	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap]
rs2393915	0.89[ASW][hapmap];0.84[MKK][hapmap]
rs2893911	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3800319	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4546474	0.85[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs6909479	0.81[AMR][1000 genomes]
rs6910659	0.81[AMR][1000 genomes]
rs6914521	0.92[AMR][1000 genomes]
rs7744605	0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7746841	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771953	0.93[EUR][1000 genomes]
rs9366689	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs9368501	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379968	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9379973	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4559087	BTN3A3	cis	parietal	SCAN
rs4559087	HIST1H4B	cis	parietal	SCAN
rs4559087	AL022393.7	cis	Muscle Skeletal	GTEx
rs4559087	ZSCAN23	cis	cerebellum	SCAN
rs4559087	ZKSCAN3	cis	parietal	SCAN
rs4559087	HIST1H2BM	cis	cerebellum	SCAN
rs4559087	BTN3A2	cis	lymphoblastoid	seeQTL
rs4559087	HIST1H2AL	cis	cerebellum	SCAN
rs4559087	ZNF323	cis	parietal	SCAN
rs4559087	ZSCAN23	cis	parietal	SCAN
rs4559087	BTN3A3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27266400-27268800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:27266400-27268800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:27266400-27269400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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