Variant report

Variant	rs7663580
Chromosome Location	chr4:85928316-85928317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85926409..85928748-chr4:85929559..85932473,2	MCF-7	breast:
2	chr4:85924417..85926451-chr4:85927021..85928799,2	MCF-7	breast:
3	chr4:85927755..85929888-chr4:85933170..85935250,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDS1-2	chr4:85927160-85932430	ENSG00000180769
2	lnc-CDS1-2	chr4:85927127-85929901	NONHSAT097259

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10029496	0.83[EUR][1000 genomes]
rs10856851	0.85[EUR][1000 genomes]
rs10856852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097026	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11097030	0.93[ASN][1000 genomes]
rs11730981	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11732309	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732347	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12498637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12498787	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503215	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12503330	0.83[EUR][1000 genomes]
rs12506456	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12510410	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12640378	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640811	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12648852	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13109918	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13114115	0.84[EUR][1000 genomes]
rs13118671	0.86[TSI][hapmap]
rs13124246	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13141322	0.85[EUR][1000 genomes]
rs13148035	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1508670	0.85[JPT][hapmap]
rs17009317	0.84[TSI][hapmap]
rs17009341	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2046404	0.91[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2869216	0.84[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap]
rs28754901	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34239067	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34314581	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131745	0.84[EUR][1000 genomes]
rs4287999	0.94[ASN][1000 genomes]
rs4376130	0.89[EUR][1000 genomes]
rs4383611	0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4470615	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4533765	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4590017	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4624645	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4626191	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4634212	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56094216	0.83[EUR][1000 genomes]
rs56194765	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531777	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6531782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531783	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs66965560	0.82[EUR][1000 genomes]
rs6833661	0.85[EUR][1000 genomes]
rs6847067	0.82[JPT][hapmap]
rs6847811	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6858666	0.83[JPT][hapmap];0.95[MEX][hapmap]
rs72664952	0.86[EUR][1000 genomes]
rs7654035	0.91[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7661609	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7675324	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682896	0.82[EUR][1000 genomes]
rs7690054	0.80[EUR][1000 genomes]
rs7692223	0.82[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs7694949	0.91[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7699226	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs9684737	0.87[EUR][1000 genomes]
rs9790649	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7663580	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:8 , 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

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