Variant report

Variant	rs6517467
Chromosome Location	chr21:16884154-16884155
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	chr21:16880501..16882055-chr21:16883399..16885226,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10854384	0.80[EUR][1000 genomes]
rs11088429	0.80[EUR][1000 genomes]
rs11911379	0.92[EUR][1000 genomes]
rs11911634	0.85[EUR][1000 genomes]
rs11911757	0.93[EUR][1000 genomes]
rs2823320	0.90[EUR][1000 genomes]
rs2823321	0.90[EUR][1000 genomes]
rs2823322	0.91[EUR][1000 genomes]
rs55675962	0.81[EUR][1000 genomes]
rs55788196	0.90[EUR][1000 genomes]
rs55817400	0.90[EUR][1000 genomes]
rs55908998	0.92[EUR][1000 genomes]
rs55936117	0.91[EUR][1000 genomes]
rs56174393	0.91[EUR][1000 genomes]
rs57843759	0.94[EUR][1000 genomes]
rs59487397	0.94[EUR][1000 genomes]
rs60282418	0.90[EUR][1000 genomes]
rs60944484	0.90[EUR][1000 genomes]
rs62217397	0.80[EUR][1000 genomes]
rs62217398	0.80[EUR][1000 genomes]
rs62217399	0.80[EUR][1000 genomes]
rs62217401	0.93[EUR][1000 genomes]
rs62217403	0.91[EUR][1000 genomes]
rs62217409	0.91[EUR][1000 genomes]
rs62217411	0.91[EUR][1000 genomes]
rs6517465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650846	0.92[EUR][1000 genomes]
rs7275233	0.81[EUR][1000 genomes]
rs7275540	0.81[EUR][1000 genomes]
rs7277561	0.81[EUR][1000 genomes]
rs7279689	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279999	0.95[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7282437	0.81[EUR][1000 genomes]
rs7282872	0.92[EUR][1000 genomes]
rs7283918	0.92[EUR][1000 genomes]
rs73187667	0.93[EUR][1000 genomes]
rs73892642	0.92[EUR][1000 genomes]
rs8127279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9305646	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979910	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9984697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1064280	chr21:16664312-17049272	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv834049	chr21:16717421-16905300	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1064621	chr21:16881027-16937290	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6517467	TMPRSS15	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16881400-16885200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr21:16881400-16885400	Weak transcription	Thymus	Thymus
3	chr21:16881400-16886000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr21:16881600-16884600	Weak transcription	Primary T cells from cord blood	blood
5	chr21:16881600-16885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:16881800-16885000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr21:16881800-16885200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr21:16881800-16885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr21:16881800-16885200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr21:16881800-16885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr21:16881800-16885400	Weak transcription	Fetal Thymus	thymus
12	chr21:16881800-16886200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr21:16882200-16884800	Weak transcription	Dnd41	blood
14	chr21:16882200-16885400	Weak transcription	HepG2	liver
15	chr21:16883800-16884600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr21:16884000-16884400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr21:16884000-16884400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr21:16884000-16884400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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