Variant report

Variant	rs3783949
Chromosome Location	chr14:81448382-81448383
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:81447196..81448849-chr14:81635444..81638287,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NRXN3-4	chr14:81448332-81449982	NONHSAT038046

Variant related genes	Relation type
ENSG00000258999	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10145099	0.99[ASN][1000 genomes]
rs1023586	0.95[ASN][1000 genomes]
rs1035144	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11159479	0.96[ASN][1000 genomes]
rs12101255	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12101261	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12323356	0.80[AMR][1000 genomes]
rs17111346	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs179262	0.83[ASN][1000 genomes]
rs179263	0.83[ASN][1000 genomes]
rs2160215	0.95[ASN][1000 genomes]
rs2215981	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2268459	0.97[ASN][1000 genomes]
rs2284726	0.99[ASN][1000 genomes]
rs2300516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2371462	0.92[CHD][hapmap]
rs2371463	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28414437	0.85[ASN][1000 genomes]
rs2888046	0.81[JPT][hapmap]
rs3783947	0.89[ASN][1000 genomes]
rs3783948	0.99[ASN][1000 genomes]
rs3783950	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411444	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4903954	0.83[JPT][hapmap]
rs4903961	0.95[ASN][1000 genomes]
rs56389234	0.97[ASN][1000 genomes]
rs6574617	0.96[ASN][1000 genomes]
rs724170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8003061	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8003515	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869348	chr14:80921098-81535754	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761847	chr14:81392124-81453137	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv456346	chr14:81399692-81448382	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
4	nsv565291	chr14:81399692-81448382	Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3783949	C14orf145	cis	cerebellum	SCAN
rs3783949	C14orf145	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81447000-81451000	Genic enhancers	Dnd41	blood
2	chr14:81447600-81448600	Enhancers	Thymus	Thymus
3	chr14:81447800-81448400	Enhancers	Aorta	Aorta
4	chr14:81447800-81448600	Enhancers	Psoas Muscle	Psoas
5	chr14:81447800-81449200	Enhancers	Placenta	Placenta
6	chr14:81448000-81453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr14:81448000-81453400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:81448200-81448600	Genic enhancers	Fetal Thymus	thymus

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