Variant report

Variant	rs34358406
Chromosome Location	chr7:38750892-38750893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10085487	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	0.80[EUR][1000 genomes]
rs10225415	0.80[EUR][1000 genomes]
rs10225550	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	1.00[ASN][1000 genomes]
rs10242407	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	0.80[EUR][1000 genomes]
rs10254873	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	1.00[ASN][1000 genomes]
rs10266279	1.00[ASN][1000 genomes]
rs10270427	1.00[AFR][1000 genomes]
rs10275873	1.00[ASN][1000 genomes]
rs10951574	0.80[EUR][1000 genomes]
rs11983387	1.00[AFR][1000 genomes]
rs12701656	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12701661	0.93[EUR][1000 genomes]
rs12701671	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224619	0.93[EUR][1000 genomes]
rs13224857	0.93[EUR][1000 genomes]
rs13229445	0.93[EUR][1000 genomes]
rs13230196	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231372	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13235997	0.93[EUR][1000 genomes]
rs13236092	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040878	0.80[EUR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[ASN][1000 genomes]
rs2189854	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2190667	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	1.00[ASN][1000 genomes]
rs2214667	0.80[EUR][1000 genomes]
rs2214668	0.80[EUR][1000 genomes]
rs2215032	1.00[AFR][1000 genomes]
rs2245773	0.80[EUR][1000 genomes]
rs2286089	0.80[EUR][1000 genomes]
rs2286093	0.80[EUR][1000 genomes]
rs2286101	0.80[EUR][1000 genomes]
rs2392599	0.80[EUR][1000 genomes]
rs2392608	1.00[ASN][1000 genomes]
rs34349310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34886315	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34997080	0.93[EUR][1000 genomes]
rs35400125	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35632362	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35816439	0.93[EUR][1000 genomes]
rs35843038	0.93[EUR][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[ASN][1000 genomes]
rs4720300	0.80[EUR][1000 genomes]
rs4723780	0.80[EUR][1000 genomes]
rs4723781	0.80[EUR][1000 genomes]
rs4723784	0.80[EUR][1000 genomes]
rs4723787	0.80[EUR][1000 genomes]
rs6462871	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6462874	1.00[ASN][1000 genomes]
rs6947695	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	0.80[EUR][1000 genomes]
rs6951429	0.80[EUR][1000 genomes]
rs6964985	1.00[ASN][1000 genomes]
rs6967384	0.80[EUR][1000 genomes]
rs6971632	1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	0.80[EUR][1000 genomes]
rs6978805	1.00[ASN][1000 genomes]
rs6979423	1.00[AFR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370730	0.93[EUR][1000 genomes]
rs7783723	1.00[ASN][1000 genomes]
rs7784065	1.00[ASN][1000 genomes]
rs7784609	1.00[ASN][1000 genomes]
rs7787423	0.80[EUR][1000 genomes]
rs7789864	1.00[ASN][1000 genomes]
rs7790054	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	1.00[ASN][1000 genomes]
rs7799887	1.00[ASN][1000 genomes]
rs7802052	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7803488	1.00[ASN][1000 genomes]
rs9638945	1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9886108	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34358406	VPS41	Cis_1M	lymphoblastoid	RTeQTL
rs34358406	FAM183B	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38748800-38756200	Weak transcription	Fetal Brain Female	brain
2	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
3	chr7:38750600-38751000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:38750600-38751000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:38750600-38751400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:38750600-38751400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:38750800-38751600	Enhancers	Pancreatic Islets	Pancreatic Islet

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