Variant report

Variant	rs12140451
Chromosome Location	chr1:215853835-215853836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215852361..215855087-chr1:215863901..215865642,2	MCF-7	breast:
2	chr1:215846715..215849694-chr1:215853458..215855866,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10864183	0.88[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11120598	0.88[CEU][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs11120605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap]
rs11120606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap]
rs11578710	0.88[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs12403674	0.84[ASW][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs12408717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1342765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2820675	0.84[JPT][hapmap]
rs2820691	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2820692	0.84[JPT][hapmap]
rs2820693	0.84[JPT][hapmap]
rs2820694	0.84[JPT][hapmap]
rs2820696	0.84[JPT][hapmap]
rs2820703	0.82[ASN][1000 genomes]
rs2886199	0.84[ASW][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs3845527	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs4372227	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4375233	0.88[JPT][hapmap]
rs4375237	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs4628479	0.88[JPT][hapmap]
rs4655285	0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4655423	0.88[JPT][hapmap]
rs6665313	0.81[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv873171	chr1:215825167-215925167	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12140451	C1orf97	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215851000-215855400	Weak transcription	Liver	Liver
2	chr1:215853200-215854400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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