Variant report

Variant	rs12028040
Chromosome Location	chr1:184227709-184227710
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184223949..184226595-chr1:184227169..184229725,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10047215	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737250	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797943	0.85[ASN][1000 genomes]
rs10797951	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797952	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797953	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911545	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911546	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911547	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911548	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911549	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911550	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911551	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911553	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10911554	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10911555	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11576933	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11579542	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11585071	0.80[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11802851	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12021761	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12046452	0.86[ASN][1000 genomes]
rs12124041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128341	0.81[ASN][1000 genomes]
rs16822656	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16822659	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1930285	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1930290	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4428848	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4651184	0.81[ASN][1000 genomes]
rs4651185	0.81[ASN][1000 genomes]
rs4651200	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs57882451	0.81[ASN][1000 genomes]
rs6424941	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424942	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424943	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661497	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666447	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66781583	0.81[ASN][1000 genomes]
rs6678439	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6684045	0.81[ASN][1000 genomes]
rs6684740	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691210	0.81[ASN][1000 genomes]
rs6693421	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696916	0.86[ASN][1000 genomes]
rs6697577	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72735619	0.81[ASN][1000 genomes]
rs72735632	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7355183	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517993	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525134	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7530243	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7543622	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932993	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs957558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963234	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs9787399	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs997343	0.81[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12028040	IVNS1ABP	cis	cerebellum	SCAN
rs12028040	STX6	cis	parietal	SCAN
rs12028040	GLT25D2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184212200-184229400	Weak transcription	NHLF	lung
2	chr1:184224200-184229000	Weak transcription	Spleen	Spleen
3	chr1:184224400-184233000	Weak transcription	Fetal Heart	heart
4	chr1:184225200-184227800	Weak transcription	Left Ventricle	heart
5	chr1:184225400-184227800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:184225400-184229000	Weak transcription	HSMM	muscle
7	chr1:184225800-184233200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:184226800-184230000	Enhancers	HUVEC	blood vessel
9	chr1:184227600-184227800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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