Variant report

Variant	rs931773
Chromosome Location	chr3:144027934-144027935
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	chr3:143689712..143692723-chr3:144026505..144028595,3	MCF-7	breast:
2	chr3:144026496..144028084-chr3:144029746..144032575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1032814	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102118	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156767	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393883	0.87[EUR][1000 genomes]
rs1725559	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725560	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725561	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183838	0.81[ASW][hapmap];0.83[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs197827	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs197828	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs197842	0.85[EUR][1000 genomes]
rs197854	0.93[EUR][1000 genomes]
rs197855	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569960	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524322	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4681214	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681649	0.87[EUR][1000 genomes]
rs4681650	0.87[EUR][1000 genomes]
rs6440239	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856786	0.86[TSI][hapmap]
rs905524	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs931772	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814110	0.87[EUR][1000 genomes]
rs9857731	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv980023	chr3:143981697-144036271	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	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
rs931773	TM4SF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144025800-144028000	Enhancers	Dnd41	blood
2	chr3:144026600-144028400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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