Variant report

Variant	rs4663988
Chromosome Location	chr2:234853128-234853129
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	chr2:234849252..234850788-chr2:234852764..234855618,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1003540	0.84[ASW][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs10166942	0.84[ASW][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs10170399	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs10189040	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10490012	0.91[MEX][hapmap]
rs10490014	0.92[ASW][hapmap];0.87[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[AFR][1000 genomes]
rs10929319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11563060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11563063	0.89[CHB][hapmap];0.88[YRI][hapmap]
rs11563216	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11892538	0.89[CHB][hapmap];0.88[YRI][hapmap]
rs1965629	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs2108809	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2362290	0.84[ASW][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2362292	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2362293	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28946911	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs28953468	0.87[CEU][hapmap]
rs4233636	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4663986	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4663990	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6431648	0.92[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs6709005	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6711120	0.84[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6712893	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6738375	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6738979	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6740118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737636	0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs758275	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs758276	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs758277	0.88[YRI][hapmap]
rs7597012	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7604471	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs887065	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs917435	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9646720	0.87[MEX][hapmap]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876024	chr2:234842650-234856421	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4663988	NMUR1	cis	parietal	SCAN
rs4663988	DIS3L2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234849400-234883400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:234849600-234873800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234851600-234854000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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