Variant report

Variant	rs12698804
Chromosome Location	chr7:69004448-69004449
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	chr7:68998151..69000333-chr7:69002849..69004454,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10256483	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10257731	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10265122	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10281633	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10487947	0.83[TSI][hapmap]
rs10950189	0.84[EUR][1000 genomes]
rs10950190	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11771876	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12155091	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530810	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12531644	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12538348	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698802	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698803	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13243683	0.86[EUR][1000 genomes]
rs13246613	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1541427	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17137493	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1981585	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1981586	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2108046	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2865169	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28758447	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35245526	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41863	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41865	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4268006	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55714924	0.85[EUR][1000 genomes]
rs56854903	0.87[EUR][1000 genomes]
rs6460521	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6944163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6946622	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975413	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6979168	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73437648	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7785268	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7810187	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12698804	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:68999800-69007400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:69000000-69014600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:69002600-69004600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:69004200-69004600	Enhancers	Fetal Intestine Small	intestine
5	chr7:69004400-69004600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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