Variant report

Variant	rs2147689
Chromosome Location	chr13:97040313-97040314
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96705085..96707362-chr13:97040004..97041510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102595	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1164587	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1410343	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1410344	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1813005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854262	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1854263	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1925103	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925106	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925109	0.84[EUR][1000 genomes]
rs1925111	0.84[EUR][1000 genomes]
rs1925132	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2151084	0.83[EUR][1000 genomes]
rs2209411	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2209412	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389657	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2389658	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2389662	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2389664	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2389665	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2389667	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2389668	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs377676	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4771251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771252	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771939	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6491288	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6491289	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330499	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7332438	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334786	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs912691	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs912692	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs912693	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs912694	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs913428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9300344	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300348	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300349	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513129	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513132	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9513133	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9516676	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9516677	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	nsv530742	chr13:96917313-97627023	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv900937	chr13:96976345-97275932	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv562792	chr13:96976345-97563413	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2147689	FARP1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97034400-97040400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr13:97034400-97040800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:97039800-97040400	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr13:97040200-97040600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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