Variant report

Variant	rs31426
Chromosome Location	chr14:79426075-79426076
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	chr14:79425453..79426658-chr14:81316149..81316920,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10873319	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs11159385	0.84[JPT][hapmap]
rs11159386	0.82[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs11159387	0.84[JPT][hapmap]
rs11159388	0.85[CHD][hapmap]
rs11159389	0.85[CHD][hapmap]
rs11159390	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs11847534	0.85[CHD][hapmap]
rs12050287	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12588364	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs149088	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs150774	0.91[CHB][hapmap]
rs154323	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs154324	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs154329	0.86[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs154330	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs154333	0.86[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs154334	0.80[ASN][1000 genomes]
rs154336	0.80[ASN][1000 genomes]
rs154340	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs154343	0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs154376	0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap]
rs154378	0.86[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap]
rs17108401	0.87[ASN][1000 genomes]
rs17108405	0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs17108413	0.87[ASN][1000 genomes]
rs17108429	0.87[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs220104	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2270963	0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs31349	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs31351	0.80[ASN][1000 genomes]
rs31352	0.80[ASN][1000 genomes]
rs31414	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs31415	0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs31417	0.87[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs31419	0.84[ASN][1000 genomes]
rs31420	0.87[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs31421	0.87[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs31422	0.87[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs31424	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs31425	0.92[EUR][1000 genomes]
rs31429	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs31436	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs31437	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs31448	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap]
rs31450	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3817535	0.86[ASN][1000 genomes]
rs61995265	0.86[ASN][1000 genomes]
rs7142134	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs7146473	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7157841	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs730024	0.84[ASN][1000 genomes]
rs8007461	0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs8011529	0.86[CHB][hapmap]

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	nsv832838	chr14:79306627-79445382	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv917249	chr14:79388181-79574717	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1041991	chr14:79394408-79644886	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1037112	chr14:79412455-79527656	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs31426	NRXN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79416800-79426200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr14:79416800-79436000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:79423600-79426200	Weak transcription	Brain Angular Gyrus	brain
4	chr14:79425800-79427000	Enhancers	Rectal Smooth Muscle	rectum
5	chr14:79426000-79426200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr14:79426000-79426200	Enhancers	Brain Hippocampus Middle	brain

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