Variant report

Variant	rs3809444
Chromosome Location	chr14:38368184-38368185
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	chr14:38365851..38368436-chr14:38371004..38373198,2	MCF-7	breast:
2	chr14:38363021..38365119-chr14:38365586..38368317,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA1-2	chr14:38365265-38368615	XLOC_010999

Variant related genes	Relation type
ENSG00000259091	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10134624	0.96[CEU][hapmap]
rs10140719	0.96[CEU][hapmap]
rs10145136	0.96[CEU][hapmap]
rs10146385	0.96[CEU][hapmap]
rs10483495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10872905	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1113092	0.96[CEU][hapmap]
rs11156973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11156974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11621735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11622986	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1170022	0.96[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs1170023	0.88[CEU][hapmap]
rs1170025	0.96[CEU][hapmap]
rs1170028	0.96[CEU][hapmap]
rs1170029	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs1170030	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1170031	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap]
rs11851837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147106	0.81[EUR][1000 genomes]
rs12432452	0.96[CEU][hapmap]
rs12435640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs12590816	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882516	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs12883466	0.82[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs17107343	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17179919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17554993	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1952787	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1952788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1952789	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs1952790	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs1958693	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1958694	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1959676	0.96[CEU][hapmap]
rs2150322	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2183531	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35272292	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143919	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4322573	0.93[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap]
rs4597229	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4898785	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4901412	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4901413	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4901421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4901422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4901423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571829	1.00[CEU][hapmap]
rs6571830	1.00[CEU][hapmap]
rs7154853	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7155891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8005651	0.96[CEU][hapmap]
rs8005895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013747	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs8014896	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap]
rs8015738	0.96[CEU][hapmap]
rs9322983	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs954881	0.80[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap]
rs9788473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9788476	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1051120	chr14:38294270-38436127	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv542046	chr14:38294270-38436127	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv564387	chr14:38357864-38563111	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv564393	chr14:38359157-38368184	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3354861	chr14:38359630-38392369	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3809444	C14orf147	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38363800-38371000	Weak transcription	Psoas Muscle	Psoas
2	chr14:38364400-38369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr14:38365000-38372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:38367800-38368200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:38368000-38368600	Enhancers	NHDF-Ad	bronchial
6	chr14:38368000-38370200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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