Variant report

Variant	rs477498
Chromosome Location	chr6:140672641-140672642
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	chr6:140670786..140673738-chr6:140751539..140753328,2	K562	blood:
2	chr6:140671269..140674164-chr6:140674183..140677907,3	K562	blood:

Extended variants
information (count: 151 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10872525	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs11155107	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1119397	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.89[ASN][1000 genomes]
rs1121833	0.94[ASN][1000 genomes]
rs12055615	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12174980	0.88[ASN][1000 genomes]
rs12660474	0.92[ASN][1000 genomes]
rs12660560	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12661752	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12662046	0.92[ASN][1000 genomes]
rs12662151	0.82[ASN][1000 genomes]
rs12662848	0.95[ASN][1000 genomes]
rs12663424	0.96[ASN][1000 genomes]
rs12663444	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663480	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12665797	0.92[ASN][1000 genomes]
rs13191189	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13192756	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13194271	0.96[ASN][1000 genomes]
rs13204703	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13207048	0.89[ASN][1000 genomes]
rs13208097	0.96[ASN][1000 genomes]
rs13213875	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13214458	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1496110	0.92[ASN][1000 genomes]
rs1496112	0.89[ASN][1000 genomes]
rs1496113	0.88[ASN][1000 genomes]
rs1519592	0.89[ASN][1000 genomes]
rs1587171	0.88[ASN][1000 genomes]
rs1603348	0.88[ASN][1000 genomes]
rs1603349	0.88[ASN][1000 genomes]
rs17053906	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17069852	0.88[ASN][1000 genomes]
rs17069854	0.88[ASN][1000 genomes]
rs17192	0.94[ASN][1000 genomes]
rs1856752	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2020197	0.84[ASN][1000 genomes]
rs2050135	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2103669	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328062	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34358600	0.84[ASN][1000 genomes]
rs34753441	0.88[ASN][1000 genomes]
rs34858573	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34984534	0.88[ASN][1000 genomes]
rs35465283	0.88[ASN][1000 genomes]
rs35626395	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35686278	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs36074095	0.88[ASN][1000 genomes]
rs4323321	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4391280	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4562159	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4637665	0.89[ASN][1000 genomes]
rs4896508	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896509	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520322	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs533610	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57291519	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62431097	0.84[ASN][1000 genomes]
rs62431100	0.84[ASN][1000 genomes]
rs62431101	0.85[ASN][1000 genomes]
rs66460448	0.83[ASN][1000 genomes]
rs71562538	0.86[ASN][1000 genomes]
rs7758187	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7761894	0.84[ASN][1000 genomes]
rs9321765	0.92[ASN][1000 genomes]
rs9321769	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373258	0.84[ASN][1000 genomes]
rs9373259	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs9373260	0.88[ASN][1000 genomes]
rs9373261	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9373262	0.89[ASN][1000 genomes]
rs9373266	0.92[ASN][1000 genomes]
rs9373267	0.90[ASN][1000 genomes]
rs9373269	0.94[ASN][1000 genomes]
rs9373270	0.94[ASN][1000 genomes]
rs9373272	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373273	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373274	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373276	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9373278	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376497	0.84[ASN][1000 genomes]
rs9376498	0.84[ASN][1000 genomes]
rs9376500	0.81[ASN][1000 genomes]
rs9376502	0.88[ASN][1000 genomes]
rs9376503	0.88[ASN][1000 genomes]
rs9376504	0.88[ASN][1000 genomes]
rs9376506	0.92[ASN][1000 genomes]
rs9376511	0.94[ASN][1000 genomes]
rs9376512	0.94[ASN][1000 genomes]
rs9376518	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385899	0.83[ASN][1000 genomes]
rs9385900	0.84[ASN][1000 genomes]
rs9385901	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs9385902	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9385903	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs9385906	0.89[ASN][1000 genomes]
rs9385908	0.96[ASN][1000 genomes]
rs9389749	0.84[ASN][1000 genomes]
rs9389750	0.84[ASN][1000 genomes]
rs9389751	0.86[ASN][1000 genomes]
rs9389753	0.88[ASN][1000 genomes]
rs9389754	0.88[ASN][1000 genomes]
rs9389755	0.88[ASN][1000 genomes]
rs9389757	0.88[ASN][1000 genomes]
rs9389760	0.88[ASN][1000 genomes]
rs9389763	0.88[ASN][1000 genomes]
rs9389767	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9389768	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9389772	0.92[ASN][1000 genomes]
rs9389773	0.90[ASN][1000 genomes]
rs9389774	0.87[ASN][1000 genomes]
rs9389775	0.81[ASN][1000 genomes]
rs9389776	0.88[ASN][1000 genomes]
rs9389777	0.89[ASN][1000 genomes]
rs9389780	0.92[ASN][1000 genomes]
rs9389781	0.92[ASN][1000 genomes]
rs9389782	0.90[ASN][1000 genomes]
rs9389783	0.92[ASN][1000 genomes]
rs9389784	0.94[ASN][1000 genomes]
rs9389785	0.94[ASN][1000 genomes]
rs9389789	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389793	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389794	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399308	0.84[ASN][1000 genomes]
rs9399310	0.89[ASN][1000 genomes]
rs9399315	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399316	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403148	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9403149	0.82[ASN][1000 genomes]
rs9403150	0.88[ASN][1000 genomes]
rs9403151	0.88[ASN][1000 genomes]
rs9403153	0.88[ASN][1000 genomes]
rs9403155	0.88[ASN][1000 genomes]
rs9403156	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9403157	0.88[ASN][1000 genomes]
rs9403159	0.89[ASN][1000 genomes]
rs9403165	0.88[ASN][1000 genomes]
rs9403168	0.90[ASN][1000 genomes]
rs9403170	0.92[ASN][1000 genomes]
rs9403171	0.94[ASN][1000 genomes]
rs9403173	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403174	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403176	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403177	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9484347	0.86[ASN][1000 genomes]
rs9791338	0.89[ASN][1000 genomes]
rs997388	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015293	chr6:140544956-140798437	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817390	chr6:140558103-141166039	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv970704	chr6:140672576-140676024	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs477498	C6orf115	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140668400-140674400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:140669000-140676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:140670600-140672800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:140671600-140672800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr6:140672200-140672800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:140672400-140672800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:140672400-140673400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:140672600-140674400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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