Variant report

Variant	rs9838616
Chromosome Location	chr3:24590841-24590842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24534792..24536707-chr3:24586895..24591064,3	K562	blood:
2	chr3:24588062..24593366-chr3:24599912..24603837,6	K562	blood:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10212332	0.84[ASN][1000 genomes]
rs10490837	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs11708042	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13318800	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561079	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs17014900	0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs17014902	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs17029611	0.81[ASN][1000 genomes]
rs1992040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992041	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2117873	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117874	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2196434	0.85[ASN][1000 genomes]
rs2196435	0.85[CEU][hapmap]
rs2196438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562279	0.82[EUR][1000 genomes]
rs3919672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs56268655	0.87[EUR][1000 genomes]
rs58152527	0.86[ASN][1000 genomes]
rs61701305	0.86[ASN][1000 genomes]
rs6550878	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6550879	1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs6767534	0.96[ASN][1000 genomes]
rs6767717	0.85[ASN][1000 genomes]
rs6769209	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770518	0.86[ASN][1000 genomes]
rs6771818	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781066	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6795607	1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs6801494	0.85[ASN][1000 genomes]
rs73038411	0.87[EUR][1000 genomes]
rs73038427	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73040438	0.85[EUR][1000 genomes]
rs73040440	0.81[EUR][1000 genomes]
rs7647700	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930317	0.85[ASN][1000 genomes]
rs9310745	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819865	0.96[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9823545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9835497	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838720	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844544	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850781	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859978	0.85[ASN][1000 genomes]
rs9861129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868375	0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9873830	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878606	0.82[JPT][hapmap];0.85[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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9838616	RPL15	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24566200-24591800	Weak transcription	Psoas Muscle	Psoas
2	chr3:24588000-24592000	Weak transcription	HepG2	liver
3	chr3:24589400-24591800	Enhancers	HSMM	muscle
4	chr3:24590400-24591800	Weak transcription	Liver	Liver
5	chr3:24590600-24591800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:24590600-24591800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:24590600-24591800	Weak transcription	HSMMtube	muscle
8	chr3:24590600-24592000	Weak transcription	NHDF-Ad	bronchial
9	chr3:24590800-24592000	Weak transcription	Stomach Mucosa	stomach

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