Variant report

Variant	rs6580699
Chromosome Location	chr12:49478812-49478813
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49478072..49490419-chr12:49518907..49527034,52	K562	blood:
2	chr12:49477289..49493962-chr12:49512467..49528127,64	K562	blood:

Variant related genes	Relation type
ENSG00000200309	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10459221	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10459232	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054442	0.85[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10783299	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10783301	0.87[ASN][1000 genomes]
rs10875910	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10875912	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875913	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875914	0.85[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs10875915	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875917	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875918	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168827	0.81[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168838	0.91[ASN][1000 genomes]
rs11168839	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs11168850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1138908	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11614738	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12298884	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12580349	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12821008	0.93[ASN][1000 genomes]
rs2117029	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2241726	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs2293445	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs2304275	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34436857	0.88[ASN][1000 genomes]
rs3741619	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs3741622	0.91[JPT][hapmap]
rs3782357	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6580698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296288	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300136	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs876333	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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6580699	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs6580699	RHEBL1	cis	cerebellum	SCAN
rs6580699	DDN	cis	Muscle Skeletal	GTEx
rs6580699	NCKAP5L	cis	parietal	SCAN
rs6580699	RHEBL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49474400-49479800	Weak transcription	HSMMtube	muscle
2	chr12:49474400-49481800	Weak transcription	HSMM	muscle
3	chr12:49476200-49481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:49478400-49480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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