Variant report

Variant	rs277406
Chromosome Location	chr5:41946529-41946530
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41940424..41943829-chr5:41945093..41947909,5	K562	blood:
2	chr5:41941926..41943756-chr5:41945285..41947330,2	K562	blood:
3	chr5:41927254..41930228-chr5:41945140..41947129,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10045473	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10051322	1.00[ASN][1000 genomes]
rs10059424	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10060170	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10062703	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10064298	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10064380	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10069638	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1006996	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10075064	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10077481	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10472357	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10941557	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1118104	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739257	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11740524	0.93[ASN][1000 genomes]
rs11744279	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11744516	0.81[ASN][1000 genomes]
rs11744623	0.93[ASN][1000 genomes]
rs11745373	0.85[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747921	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1175227	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357951	1.00[ASN][1000 genomes]
rs13360001	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1355089	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508816	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533014	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1567323	0.81[ASN][1000 genomes]
rs16871972	0.93[ASN][1000 genomes]
rs17739462	0.93[ASN][1000 genomes]
rs17847285	0.93[ASN][1000 genomes]
rs1876654	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2113053	1.00[ASN][1000 genomes]
rs2231910	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2231917	1.00[ASN][1000 genomes]
rs2329815	0.93[ASN][1000 genomes]
rs276315	0.95[GIH][hapmap];0.86[TSI][hapmap]
rs277407	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277414	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277416	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316724	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34339137	0.93[ASN][1000 genomes]
rs34663371	0.93[ASN][1000 genomes]
rs35077044	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35154057	0.93[ASN][1000 genomes]
rs35252930	0.81[ASN][1000 genomes]
rs35613904	0.93[ASN][1000 genomes]
rs4050986	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4289604	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324728	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4957171	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957173	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957174	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957175	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957176	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957177	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957178	1.00[ASN][1000 genomes]
rs4957180	1.00[ASN][1000 genomes]
rs4957422	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957423	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957424	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957428	0.93[ASN][1000 genomes]
rs4957429	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957430	0.93[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957432	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957433	1.00[ASN][1000 genomes]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957436	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957437	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957438	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957439	1.00[ASN][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs6451581	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6451582	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66820325	0.93[ASN][1000 genomes]
rs67114999	0.93[ASN][1000 genomes]
rs676067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881873	0.93[ASN][1000 genomes]
rs6889217	1.00[JPT][hapmap]
rs72746983	1.00[ASN][1000 genomes]
rs72746996	1.00[ASN][1000 genomes]
rs7712911	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7728482	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729014	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7733096	0.93[ASN][1000 genomes]
rs9292825	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[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	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
2	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
4	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs277406	LIFR	cis	cerebellum	SCAN
rs277406	C5orf39	cis	cerebellum	SCAN
rs277406	NUDC	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41926000-41951400	Weak transcription	Gastric	stomach
2	chr5:41926200-41946800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:41926200-41947000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:41936200-41946600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:41936600-41951400	Weak transcription	Aorta	Aorta
6	chr5:41936600-41951400	Weak transcription	Left Ventricle	heart
7	chr5:41946000-41947200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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