Variant report

Variant	rs197854
Chromosome Location	chr3:144040392-144040393
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	chr3:143940644..143942210-chr3:144039456..144041845,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1032814	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1102118	0.83[EUR][1000 genomes]
rs1156767	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1393883	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1608999	0.82[CHB][hapmap]
rs1725559	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1725560	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1725561	0.89[EUR][1000 genomes]
rs183838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197826	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs197828	0.83[EUR][1000 genomes]
rs197829	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs197832	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs197842	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197855	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2134594	0.85[AMR][1000 genomes]
rs2569960	0.95[EUR][1000 genomes]
rs4524322	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681214	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4681649	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681650	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440239	0.93[EUR][1000 genomes]
rs856786	0.86[TSI][hapmap]
rs905524	0.82[AMR][1000 genomes]
rs931772	0.93[EUR][1000 genomes]
rs931773	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs9814110	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9835986	0.82[CHB][hapmap]
rs9878391	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1002032	chr3:143848755-144065468	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877570	chr3:143853149-144123401	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv591926	chr3:143873901-144058395	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1011685	chr3:143959237-144218424	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv536751	chr3:143959237-144218424	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv591927	chr3:143998527-144054686	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs197854	TM4SF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144040000-144040600	Enhancers	HSMMtube	muscle
2	chr3:144040200-144040600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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