Variant report

Variant	rs1400593
Chromosome Location	chr12:118051578-118051579
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	chr12:118014276..118016449-chr12:118050467..118052138,2	K562	blood:
2	chr12:118046298..118048327-chr12:118049389..118052295,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10444499	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735108	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735110	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10735111	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10774940	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068589	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12826831	0.83[ASN][1000 genomes]
rs1400589	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1517196	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517204	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568154	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1568158	0.89[EUR][1000 genomes]
rs1568160	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1568161	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1850403	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976755	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090440	0.82[EUR][1000 genomes]
rs2138697	0.86[AFR][1000 genomes]
rs2138698	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2393240	0.89[EUR][1000 genomes]
rs2393250	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2393251	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650169	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4553436	0.80[EUR][1000 genomes]
rs4570668	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4767580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4767581	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4767586	0.92[EUR][1000 genomes]
rs4767587	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6490130	0.86[EUR][1000 genomes]
rs6490131	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490137	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6490139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6490142	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs708861	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7298395	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7305557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7399212	0.84[EUR][1000 genomes]
rs7957425	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980301	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816195	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs860113	0.85[EUR][1000 genomes];0.86[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	nsv832527	chr12:117974007-118110244	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1400593	VSIG10	cis	parietal	SCAN
rs1400593	SDSL	cis	parietal	SCAN
rs1400593	NIP30	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118051400-118051600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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