Variant report

Variant	rs6531783
Chromosome Location	chr4:85932343-85932344
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	chr4:85926409..85928748-chr4:85929559..85932473,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDS1-2	chr4:85927160-85932430	ENSG00000180769

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10856852	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11097028	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11732309	0.83[EUR][1000 genomes]
rs11732347	0.83[EUR][1000 genomes]
rs12498787	0.82[EUR][1000 genomes]
rs12500519	0.84[EUR][1000 genomes]
rs12502559	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12503330	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12640378	0.81[EUR][1000 genomes]
rs13118671	0.87[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13125323	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13139541	0.90[EUR][1000 genomes]
rs13141072	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1484661	0.82[JPT][hapmap]
rs1508670	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17009317	0.80[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs17009334	0.90[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs17009341	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2046404	0.86[JPT][hapmap]
rs28754901	0.80[EUR][1000 genomes]
rs34239067	0.81[EUR][1000 genomes]
rs35190829	0.85[EUR][1000 genomes]
rs35892581	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4383611	0.93[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533765	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4590017	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4626191	0.82[EUR][1000 genomes]
rs55871210	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55912355	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56094216	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56194765	0.83[EUR][1000 genomes]
rs58074983	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6531777	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs6531782	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs66965560	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67624868	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6815917	0.91[EUR][1000 genomes]
rs6820517	0.93[EUR][1000 genomes]
rs6829807	0.84[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs71631375	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72664928	0.83[EUR][1000 genomes]
rs72664957	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7654035	0.86[JPT][hapmap]
rs7661609	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs7663580	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7675324	0.82[EUR][1000 genomes]
rs7682896	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7690054	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692223	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7694949	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs7695054	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7699226	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs9790649	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3367963	chr4:85911017-86246036	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6531783	NCRNA00247	cis	cerebellum	SCAN
rs6531783	HERC5	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85915800-85935600	Weak transcription	Aorta	Aorta
2	chr4:85925400-85935400	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:85925400-85940600	Weak transcription	Left Ventricle	heart
4	chr4:85925800-85932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:85927400-85933000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:85927400-85935400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:85927800-85933200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:85927800-85935600	Weak transcription	Ovary	ovary
9	chr4:85932000-85932600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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