Variant report

Variant	rs17700072
Chromosome Location	chr7:38750986-38750987
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POU6F2-2	chr7:38750901-38751632	NONHSAT120190

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1017028	0.83[ASN][1000 genomes]
rs10242048	0.83[ASN][1000 genomes]
rs10247503	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10251912	0.86[ASN][1000 genomes]
rs10254567	0.86[ASN][1000 genomes]
rs10271176	0.86[ASN][1000 genomes]
rs10486677	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10486678	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs11971020	0.85[ASN][1000 genomes]
rs11979618	0.94[ASN][1000 genomes]
rs11979824	0.85[ASN][1000 genomes]
rs11980882	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12533557	0.86[ASN][1000 genomes]
rs12667567	0.88[ASN][1000 genomes]
rs12672237	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12672750	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12672793	0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12672885	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs12701652	0.80[JPT][hapmap]
rs12701659	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1468348	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700142	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17700172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700190	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17700262	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs17700392	0.85[ASN][1000 genomes]
rs17700752	0.87[YRI][hapmap]
rs17767695	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17767770	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17767818	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs17768153	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs17768212	0.85[ASN][1000 genomes]
rs17768711	0.84[CHB][hapmap]
rs1859494	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1859937	0.81[JPT][hapmap]
rs1864886	0.81[JPT][hapmap]
rs1978171	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978172	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074655	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2074657	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs2107743	0.86[ASN][1000 genomes]
rs2189855	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs2214666	0.85[ASN][1000 genomes]
rs2240351	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2240352	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2240353	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2240354	0.84[ASN][1000 genomes]
rs2286082	0.85[ASN][1000 genomes]
rs2286084	0.85[ASN][1000 genomes]
rs2286086	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2286087	0.85[ASN][1000 genomes]
rs2286088	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs2286091	0.85[ASN][1000 genomes]
rs2286094	0.84[ASN][1000 genomes]
rs2286098	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2286104	0.85[ASN][1000 genomes]
rs2286105	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2286106	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2286109	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2392598	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs28548028	0.86[ASN][1000 genomes]
rs34724372	0.82[CHB][hapmap]
rs35253728	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35791079	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735347	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801139	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3801140	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3801141	0.85[ASN][1000 genomes]
rs3801143	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3801145	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3801146	0.86[ASN][1000 genomes]
rs4723782	0.86[ASN][1000 genomes]
rs4723785	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs56050717	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57091471	0.85[ASN][1000 genomes]
rs60590111	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62444078	0.84[ASN][1000 genomes]
rs62444107	0.85[ASN][1000 genomes]
rs6462860	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs66662538	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs66796288	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66976998	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs67202646	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs733150	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs73368205	0.83[ASN][1000 genomes]
rs7778570	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779329	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7780625	0.80[JPT][hapmap]
rs7783546	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7783695	0.86[JPT][hapmap]
rs7785911	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7786389	0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs7794030	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7795874	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7797871	0.96[ASN][1000 genomes]
rs7810938	0.80[ASN][1000 genomes]
rs886646	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17700072	VPS41	Cis_1M	lymphoblastoid	RTeQTL

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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