Variant report

Variant	rs4902459
Chromosome Location	chr14:39724874-39724875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39723480..39726752-chr14:39734420..39736573,4	MCF-7	breast:
2	chr14:39723236..39725600-chr14:39735576..39738521,2	K562	blood:
3	chr14:39723302..39725230-chr14:39733033..39735981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000258941	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10137623	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10142479	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142523	0.83[ASN][1000 genomes]
rs10144445	0.80[ASN][1000 genomes]
rs11622951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12433610	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs12881376	0.86[ASN][1000 genomes]
rs1570131	0.80[ASW][hapmap]
rs17092065	0.83[ASN][1000 genomes]
rs1980609	0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1998193	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2025027	0.89[JPT][hapmap]
rs2025028	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs28502509	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4902460	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61998553	0.86[ASN][1000 genomes]
rs6571911	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571912	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571921	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs7141840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7147869	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153074	0.89[ASW][hapmap];0.90[JPT][hapmap]
rs7153523	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs7154632	1.00[ASW][hapmap]
rs8006319	0.90[ASN][1000 genomes]
rs9322996	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9743804	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902459	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39703600-39735400	Weak transcription	Pancreas	Pancrea
2	chr14:39704400-39734400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr14:39718600-39728000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:39721600-39725200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:39721600-39728000	Weak transcription	Fetal Intestine Small	intestine
6	chr14:39722800-39726000	Weak transcription	Liver	Liver
7	chr14:39724200-39728000	Weak transcription	Fetal Intestine Large	intestine
8	chr14:39724600-39725400	Strong transcription	HepG2	liver

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