Variant report

Variant	rs4318054
Chromosome Location	chr12:33098236-33098237
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	chr12:33097948..33099540-chr12:33236195..33238566,2	MCF-7	breast:
2	chr12:32907372..32910598-chr12:33095845..33098842,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139131	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1032702	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032703	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032704	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772016	0.83[YRI][hapmap]
rs10844411	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10844428	0.85[EUR][1000 genomes]
rs11052314	0.83[YRI][hapmap]
rs11052390	0.84[EUR][1000 genomes]
rs11052399	0.83[EUR][1000 genomes]
rs11608737	0.83[EUR][1000 genomes]
rs1353934	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1353935	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1500073	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1846638	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs1909610	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909611	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35969824	0.95[EUR][1000 genomes]
rs4394915	0.83[YRI][hapmap]
rs4931672	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6488115	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295724	0.86[EUR][1000 genomes]
rs7305797	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305861	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7306057	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306202	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7315188	0.90[EUR][1000 genomes]
rs7977438	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7977579	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs904640	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9738114	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9739928	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs985876	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs985877	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][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	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv832367	chr12:33063644-33298967	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4318054	H3F3C	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33097200-33098400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:33097400-33103000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:33098200-33100200	Enhancers	Placenta	Placenta

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