Variant report

Variant	rs1460756
Chromosome Location	chr4:87182910-87182911
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	chr4:87134159..87136485-chr4:87181961..87184950,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10009161	0.87[AFR][1000 genomes]
rs10016847	0.87[AFR][1000 genomes]
rs10019871	0.87[AFR][1000 genomes]
rs10021706	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10025305	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029339	0.94[ASW][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs10034428	0.94[ASW][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs11097102	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs11097103	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs11935211	0.92[AFR][1000 genomes]
rs12500319	0.84[AFR][1000 genomes]
rs12646076	0.84[AFR][1000 genomes]
rs1460750	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs1460757	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460758	0.90[YRI][hapmap];0.92[AFR][1000 genomes]
rs1460759	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs1460760	0.81[ASW][hapmap];0.85[LWK][hapmap]
rs1460763	0.82[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs1599313	0.94[ASW][hapmap];0.85[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs17011421	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs2035057	0.86[AFR][1000 genomes]
rs2199309	0.82[ASW][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs2869421	0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs28812808	0.90[AFR][1000 genomes]
rs6531905	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs6531906	0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs6531907	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs6531909	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs6531910	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs6531911	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs6531912	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531913	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817452	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs6825521	0.91[AFR][1000 genomes]
rs6827698	0.94[ASW][hapmap];0.85[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs6828947	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs6829870	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs6832259	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs6844365	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs6845605	0.93[AFR][1000 genomes]
rs6845742	0.93[AFR][1000 genomes]
rs7440491	0.82[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap]
rs7655797	0.87[AFR][1000 genomes]
rs7657056	0.82[AFR][1000 genomes]
rs7665868	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666231	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7668374	0.94[ASW][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs7669487	0.87[AFR][1000 genomes]
rs7680934	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs7687771	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs7699047	0.85[AFR][1000 genomes]
rs922195	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9884127	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs9996693	0.87[AFR][1000 genomes]
rs9999403	0.90[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	esv2763374	chr4:87151085-87184332	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1460756	ABCG2	cis	parietal	SCAN
rs1460756	SCD5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87149200-87186200	Weak transcription	Ovary	ovary
2	chr4:87155200-87185400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:87179200-87185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:87179800-87183800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:87182400-87183000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr4:87182400-87183200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:87182400-87183200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:87182400-87183400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:87182600-87183200	Enhancers	Osteobl	bone
10	chr4:87182800-87183000	Enhancers	Brain Germinal Matrix	brain

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