Variant report

Variant	rs6861560
Chromosome Location	chr5:44708378-44708379
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	chr5:44705749..44708436-chr5:44708902..44711292,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10447145	0.86[EUR][1000 genomes]
rs1048758	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1061310	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs11741772	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11746506	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11747159	0.81[ASN][1000 genomes]
rs11949847	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12188871	0.87[CHB][hapmap]
rs12515012	0.97[EUR][1000 genomes]
rs12651949	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs13155698	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs13159598	0.82[JPT][hapmap]
rs13174122	0.82[JPT][hapmap]
rs13177711	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs13179137	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13185555	0.88[EUR][1000 genomes]
rs13189120	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs1371025	0.86[JPT][hapmap]
rs1438819	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1438820	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1438825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438827	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs16901937	0.96[EUR][1000 genomes]
rs1866406	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1898701	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2165009	0.97[EUR][1000 genomes]
rs2218080	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2218081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2330572	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761648	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs3761650	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4457089	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6451770	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6868232	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6872254	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs6896350	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs714130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs727304	0.85[CHB][hapmap]
rs727305	0.87[CHB][hapmap]
rs7716571	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7717459	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs7720787	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs920329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9637783	0.81[CHB][hapmap];0.86[JPT][hapmap]

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	nsv830278	chr5:44540863-44713312	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv880457	chr5:44632008-44800665	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830279	chr5:44688175-44860815	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6861560	RP11-53O19.3	cis	Nerve Tibial	GTEx
rs6861560	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44706800-44729200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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