Variant report

Variant	rs6495337
Chromosome Location	chr15:79125689-79125690
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79124240..79126508-chr15:79129753..79131723,2	MCF-7	breast:
2	chr15:79119050..79121049-chr15:79123408..79126326,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11072810	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072811	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11632963	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11852830	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903613	0.99[EUR][1000 genomes]
rs12903668	0.99[EUR][1000 genomes]
rs12908341	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28505515	0.81[ASN][1000 genomes]
rs4539564	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551997	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62011004	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495338	0.83[ASN][1000 genomes]
rs6495339	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495340	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166405	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7168915	0.86[EUR][1000 genomes]
rs7169511	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173743	0.91[GIH][hapmap];0.80[MEX][hapmap]
rs7178750	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024048	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030937	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032771	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032842	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032908	0.82[ASN][1000 genomes]
rs8034274	0.84[EUR][1000 genomes]
rs8034804	0.99[EUR][1000 genomes]
rs8035039	0.99[EUR][1000 genomes]
rs9920324	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6495337	CLK3	cis	parietal	SCAN
rs6495337	CPLX3	cis	cerebellum	SCAN
rs6495337	CTSH	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79118400-79138400	Weak transcription	Right Atrium	heart
2	chr15:79118800-79128400	Weak transcription	Ovary	ovary
3	chr15:79123000-79130400	Weak transcription	Left Ventricle	heart
4	chr15:79123800-79127200	Weak transcription	Gastric	stomach
5	chr15:79124400-79130200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:79125200-79133000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:79125400-79125800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:79125600-79130600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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