Variant report

Variant	rs2472530
Chromosome Location	chr11:5153261-5153262
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:5150178..5155699-chr11:5220911..5225581,8	K562	blood:
2	chr11:5143364..5146967-chr11:5150857..5153670,3	K562	blood:
3	chr11:5151510..5153269-chr11:5386500..5388516,2	K562	blood:
4	chr11:5150860..5154299-chr11:5221551..5224711,3	K562	blood:
5	chr11:5151017..5154048-chr11:5172575..5176593,5	K562	blood:
6	chr11:5150699..5153690-chr11:5165729..5169449,3	K562	blood:
7	11:5146608-5154908..11:5349791-5355747	K562	blood:
8	chr11:5140099..5148928-chr11:5149317..5155604,15	K562	blood:
9	chr11:5150718..5153704-chr11:5259366..5262458,3	K562	blood:
10	chr11:5151592..5153371-chr11:5383918..5386236,2	K562	blood:
11	chr11:5151728..5155807-chr11:5263615..5268276,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236359	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000205494	Chromatin interaction
ENSG00000182070	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000176742	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10500616	0.81[JPT][hapmap]
rs10500617	0.81[JPT][hapmap]
rs10768550	0.81[JPT][hapmap]
rs10837295	0.84[JPT][hapmap]
rs10837329	0.86[JPT][hapmap]
rs10837334	0.84[JPT][hapmap]
rs10837450	0.84[AMR][1000 genomes]
rs10837461	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10837508	1.00[ASW][hapmap];0.82[CHB][hapmap]
rs11035765	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs11035774	0.81[JPT][hapmap]
rs11036090	0.82[CHB][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs11036814	1.00[LWK][hapmap]
rs12221996	0.84[JPT][hapmap]
rs1463381	0.85[JPT][hapmap]
rs2472522	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2472526	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472527	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2499947	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2499948	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2499949	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2499950	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2499951	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002636	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294557	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs4370933	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs4910715	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs6578556	0.81[CHB][hapmap]
rs6578559	0.81[CHB][hapmap]
rs7350513	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs7940626	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv896920	chr11:5068137-5221825	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv896923	chr11:5091882-5199208	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv896924	chr11:5098714-5221825	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv467668	chr11:5138733-5207389	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
10	nsv553224	chr11:5138733-5207389	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
11	nsv896925	chr11:5140977-5221825	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
12	nsv896926	chr11:5143309-5170510	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2472530	SYT8	cis	parietal	SCAN
rs2472530	OR56A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5152800-5154000	Flanking Active TSS	K562	blood

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