Variant report

Variant	rs4923838
Chromosome Location	chr15:40004273-40004274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40002140..40004619-chr15:40006092..40009009,2	K562	blood:
2	chr15:40004259..40006236-chr15:40010388..40013115,2	MCF-7	breast:
3	chr15:39984467..39987996-chr15:40003626..40006912,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1073675	1.00[CEU][hapmap]
rs11858148	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12437837	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12440567	0.85[JPT][hapmap]
rs16952186	0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs16969621	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs16969662	1.00[CEU][hapmap]
rs16969663	1.00[CEU][hapmap]
rs16969664	1.00[CEU][hapmap]
rs16969666	1.00[CEU][hapmap]
rs16969672	1.00[CEU][hapmap]
rs16969679	1.00[CEU][hapmap]
rs16969680	1.00[CEU][hapmap]
rs16969688	1.00[CEU][hapmap]
rs16969789	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs16969802	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1906166	0.84[ASN][1000 genomes]
rs2129457	0.81[CEU][hapmap]
rs2171312	0.85[JPT][hapmap]
rs4924379	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs4924380	0.93[CHB][hapmap]
rs4924383	0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs4924387	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs59180773	0.99[ASN][1000 genomes]
rs59434895	0.83[ASN][1000 genomes]
rs60431166	0.83[ASN][1000 genomes]
rs61620785	0.95[ASN][1000 genomes]
rs61695850	0.83[ASN][1000 genomes]
rs7172155	1.00[CEU][hapmap]
rs7173020	0.95[ASN][1000 genomes]
rs7173948	1.00[CEU][hapmap]
rs7181354	1.00[CEU][hapmap]
rs7182423	1.00[CEU][hapmap]
rs72727050	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024166	0.93[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs8032864	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8034520	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs8034550	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8035291	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs8035986	0.91[ASN][1000 genomes]
rs8041266	1.00[CEU][hapmap]
rs937961	1.00[CEU][hapmap]
rs937962	1.00[CEU][hapmap]
rs951374	0.91[ASN][1000 genomes]

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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4923838	CASC5	cis	parietal	SCAN
rs4923838	VPS18	cis	parietal	SCAN
rs4923838	GPR176	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39999800-40004400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:40000200-40005400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:40001200-40004800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:40001200-40011800	Weak transcription	NHDF-Ad	bronchial
5	chr15:40003600-40011200	Weak transcription	Osteobl	bone

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