Variant report

Variant	rs2084507
Chromosome Location	chr3:159079542-159079543
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	chr3:159078707..159080355-chr3:159081037..159083435,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1122205	0.85[YRI][hapmap]
rs11715734	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13074822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1349165	0.85[YRI][hapmap]
rs1349166	0.85[YRI][hapmap]
rs1375403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1375404	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1375405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1448998	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1449012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1449018	0.81[YRI][hapmap]
rs1449019	0.85[YRI][hapmap]
rs1449024	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1449027	0.83[CHB][hapmap]
rs1562669	0.85[YRI][hapmap]
rs1562671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1562672	0.83[CHB][hapmap]
rs17795566	0.83[CHB][hapmap]
rs1868415	0.81[YRI][hapmap]
rs1975601	0.83[CHB][hapmap]
rs2365820	0.87[YRI][hapmap]
rs2365821	0.85[YRI][hapmap]
rs2595232	0.83[CHB][hapmap]
rs2595236	0.83[CHB][hapmap]
rs2595242	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap]
rs2595243	0.83[CHB][hapmap]
rs2595244	0.83[CHB][hapmap]
rs2595245	0.83[CHB][hapmap]
rs2595246	0.82[CHB][hapmap]
rs2595247	0.91[CHB][hapmap]
rs2595248	0.87[CHB][hapmap]
rs2621284	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs2621290	0.86[CHB][hapmap]
rs2621294	0.83[CHB][hapmap]
rs2621295	0.83[CHB][hapmap]
rs2621297	0.83[CHB][hapmap]
rs2621299	0.83[CHB][hapmap]
rs2621300	0.82[CHB][hapmap]
rs2621306	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs2621310	0.87[CHB][hapmap]
rs2621312	0.87[CHB][hapmap]
rs2621313	0.87[CHB][hapmap]
rs2621314	0.87[CHB][hapmap]
rs4680500	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6441254	0.85[YRI][hapmap]
rs6441255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6782867	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6787941	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6807076	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs6810169	0.85[YRI][hapmap]
rs73166247	0.97[ASN][1000 genomes]
rs733904	0.99[ASN][1000 genomes]
rs7428369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7611870	0.85[YRI][hapmap]
rs7629577	0.85[YRI][hapmap]
rs7629583	0.85[YRI][hapmap]
rs7646959	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs7649056	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9283611	0.85[YRI][hapmap]
rs9681445	0.85[YRI][hapmap]
rs9809459	0.85[YRI][hapmap]
rs9825664	0.85[YRI][hapmap]
rs9855118	0.85[YRI][hapmap]
rs9855265	0.95[CEU][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2084507	LEKR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159076400-159080000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:159076400-159080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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