Variant report

Variant	rs873107
Chromosome Location	chr15:50101072-50101073
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	chr15:50099998..50102437-chr15:50104715..50106817,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DTWD1-6	chr15:50100869-50101106	expReg_chr15_3100_+

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11070724	0.94[ASN][1000 genomes]
rs11070727	0.91[ASN][1000 genomes]
rs11070728	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070729	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070731	0.90[ASN][1000 genomes]
rs11634432	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634466	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634538	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11635995	0.92[ASN][1000 genomes]
rs11855340	0.92[ASN][1000 genomes]
rs11858914	0.86[ASN][1000 genomes]
rs12438404	0.89[ASN][1000 genomes]
rs12440711	0.92[ASN][1000 genomes]
rs12441351	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs12442186	0.96[ASN][1000 genomes]
rs12442880	0.92[ASN][1000 genomes]
rs12904515	0.98[ASN][1000 genomes]
rs12909601	0.96[ASN][1000 genomes]
rs12911756	0.94[ASN][1000 genomes]
rs12912869	0.94[ASN][1000 genomes]
rs1395882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1395883	0.98[ASN][1000 genomes]
rs1395885	0.98[ASN][1000 genomes]
rs1395886	0.98[ASN][1000 genomes]
rs1507584	0.98[ASN][1000 genomes]
rs1507585	0.98[ASN][1000 genomes]
rs1507586	0.98[ASN][1000 genomes]
rs1588122	0.98[ASN][1000 genomes]
rs1828041	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1828042	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1848282	0.98[ASN][1000 genomes]
rs1848283	0.98[ASN][1000 genomes]
rs1848284	0.98[ASN][1000 genomes]
rs2102383	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413967	0.91[ASN][1000 genomes]
rs2413968	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2413969	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2413970	0.90[ASN][1000 genomes]
rs2413971	0.86[ASN][1000 genomes]
rs2452534	0.82[ASN][1000 genomes]
rs2452535	0.98[ASN][1000 genomes]
rs2452537	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452538	0.98[ASN][1000 genomes]
rs2456840	0.98[ASN][1000 genomes]
rs2456841	0.98[ASN][1000 genomes]
rs2456842	0.96[ASN][1000 genomes]
rs2660966	0.98[ASN][1000 genomes]
rs2899438	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34614239	0.90[ASN][1000 genomes]
rs34696884	0.81[ASN][1000 genomes]
rs35816674	0.96[ASN][1000 genomes]
rs35861473	0.96[ASN][1000 genomes]
rs4404008	0.92[ASN][1000 genomes]
rs4526969	0.92[ASN][1000 genomes]
rs4551980	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs4774546	0.90[ASN][1000 genomes]
rs4774547	0.84[ASN][1000 genomes]
rs4774548	0.81[ASN][1000 genomes]
rs71124308	0.90[ASN][1000 genomes]
rs7182178	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs7182911	0.93[ASN][1000 genomes]
rs8039234	0.92[ASN][1000 genomes]
rs937169	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1528	chr15:50067958-50112958	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1047047	chr15:50070224-50125096	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1042311	chr15:50083175-50125096	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2761888	chr15:50083187-50125108	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542381	chr15:50086150-50115876	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs873107	SPG11	cis	parietal	SCAN
rs873107	DTWD1	cis	cerebellum	SCAN
rs873107	CEP152	cis	cerebellum	SCAN
rs873107	PATL2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50098000-50101200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:50100400-50103200	Enhancers	Hela-S3	cervix

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