Variant report

Variant	rs17034880
Chromosome Location	chr12:104310867-104310868
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104309475..104312400-chr12:104350529..104352590,2	MCF-7	breast:
2	chr12:104309007..104311155-chr12:104321580..104324192,3	K562	blood:

Variant related genes	Relation type
ENSG00000166598	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10778306	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11111845	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11612613	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12422615	1.00[MKK][hapmap]
rs12426161	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12426382	0.82[CHB][hapmap]
rs12427041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582800	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12582917	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1550207	1.00[MKK][hapmap]
rs17034637	1.00[MKK][hapmap]
rs17034639	1.00[MKK][hapmap]
rs17034640	1.00[MKK][hapmap]
rs17034642	1.00[MKK][hapmap]
rs17034645	1.00[MKK][hapmap]
rs17034648	1.00[MKK][hapmap]
rs17034662	1.00[MKK][hapmap]
rs17034911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034946	1.00[AFR][1000 genomes]
rs17035153	1.00[MKK][hapmap]
rs17180749	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs17192854	1.00[MKK][hapmap]
rs17794246	1.00[MKK][hapmap]
rs17795947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1882019	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs2293626	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs2576942	0.88[JPT][hapmap]
rs2722189	0.88[JPT][hapmap]
rs3751207	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs3751208	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs3829300	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs4135060	1.00[AFR][1000 genomes]
rs4135076	1.00[AFR][1000 genomes]
rs4135078	1.00[AFR][1000 genomes]
rs4135082	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs4135085	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs4135086	1.00[AFR][1000 genomes]
rs4135087	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs4135094	1.00[AFR][1000 genomes]
rs4135095	1.00[AFR][1000 genomes]
rs55919036	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56040534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59879726	0.82[ASN][1000 genomes]
rs60534873	1.00[AFR][1000 genomes]
rs6615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728167	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9788014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17034880	NFYB	cis	cerebellum	SCAN
rs17034880	GNN	cis	parietal	SCAN
rs17034880	HCFC2	cis	cerebellum	SCAN
rs17034880	ACTR6	cis	cerebellum	SCAN
rs17034880	GLT8D2	cis	parietal	SCAN
rs17034880	NT5DC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104306200-104320800	Weak transcription	Psoas Muscle	Psoas

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