Variant report

Variant	rs1001684
Chromosome Location	chr5:40810426-40810427
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40805017..40807937-chr5:40809929..40811928,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1002423	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1002424	0.81[ASW][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10041430	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043245	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065570	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10074991	0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1122655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11956047	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957736	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13361707	0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1345778	0.85[GIH][hapmap]
rs2329353	0.83[GIH][hapmap]
rs249440	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs28544962	0.84[AMR][1000 genomes]
rs3763074	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3805487	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs3805497	1.00[YRI][hapmap]
rs4957352	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58692207	0.84[AMR][1000 genomes]
rs58751240	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59133000	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59338019	0.84[AMR][1000 genomes]
rs6868517	0.81[CHB][hapmap];0.85[GIH][hapmap];0.82[YRI][hapmap]
rs6876367	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6899032	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73084490	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705504	0.82[YRI][hapmap]
rs7717357	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[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	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1001684	NUP155	cis	parietal	SCAN
rs1001684	FGF10	cis	parietal	SCAN
rs1001684	RPL37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40808400-40826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:40808600-40814000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:40808800-40825600	Weak transcription	HSMM	muscle
4	chr5:40809000-40813800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:40809200-40811400	Weak transcription	K562	blood
6	chr5:40810000-40810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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