Variant report

Variant	rs4288425
Chromosome Location	chr8:91374274-91374275
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	chr8:91366748..91369892-chr8:91373800..91376139,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10441528	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10956589	0.96[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10956590	0.96[CEU][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12542159	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12548764	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12677381	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13263139	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16904390	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16904410	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs16904419	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2005936	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2189254	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35373684	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3863251	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3934716	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3934717	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236770	0.81[CEU][hapmap]
rs4263818	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4286991	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4364677	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4379493	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4510907	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4527927	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534167	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4554514	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4567086	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4576466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs4734084	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4734447	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4734449	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4734540	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734541	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734704	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734706	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734718	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4735609	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61582074	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6470976	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6470995	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470998	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6470999	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471000	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6988658	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6996909	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7009336	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7009723	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7014679	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727099	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7460798	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7822035	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7827909	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7829290	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7844648	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845673	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975976	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018991	chr8:91336887-91374274	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4288425	MMP16	cis	parietal	SCAN
rs4288425	DECR1	cis	parietal	SCAN
rs4288425	RUNX1T1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91365200-91375800	Weak transcription	K562	blood
2	chr8:91373400-91374800	Enhancers	Fetal Brain Male	brain
3	chr8:91373400-91374800	Enhancers	Fetal Brain Female	brain
4	chr8:91373600-91374600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr8:91373600-91374800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr8:91373600-91375000	Enhancers	Brain Germinal Matrix	brain
7	chr8:91374000-91374400	Enhancers	Ovary	ovary
8	chr8:91374200-91374400	Enhancers	Brain Angular Gyrus	brain
9	chr8:91374200-91374400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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