Variant report

Variant	rs4959050
Chromosome Location	chr6:30416831-30416832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30415302..30418095-chr6:30418692..30421060,4	K562	blood:
2	chr6:30311595..30314515-chr6:30415141..30417172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10947078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11752542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11753256	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11756630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11963959	0.82[EUR][1000 genomes]
rs11968858	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12180542	0.81[EUR][1000 genomes]
rs17411284	0.82[EUR][1000 genomes]
rs17411410	0.82[EUR][1000 genomes]
rs17411480	0.82[EUR][1000 genomes]
rs2077572	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2077573	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2078677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2428536	0.82[EUR][1000 genomes]
rs34090585	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34101875	0.81[EUR][1000 genomes]
rs34163258	0.81[EUR][1000 genomes]
rs34186179	0.81[EUR][1000 genomes]
rs34335619	0.81[EUR][1000 genomes]
rs34340584	0.81[EUR][1000 genomes]
rs34435337	0.81[EUR][1000 genomes]
rs34551551	0.81[EUR][1000 genomes]
rs34552114	0.82[EUR][1000 genomes]
rs34708826	0.82[EUR][1000 genomes]
rs34727270	0.81[EUR][1000 genomes]
rs34762601	0.81[EUR][1000 genomes]
rs34960122	0.82[EUR][1000 genomes]
rs35227387	0.81[EUR][1000 genomes]
rs35230915	0.81[EUR][1000 genomes]
rs35235619	0.82[EUR][1000 genomes]
rs35268644	0.81[EUR][1000 genomes]
rs35328743	0.82[EUR][1000 genomes]
rs35365548	0.81[EUR][1000 genomes]
rs35407515	0.82[EUR][1000 genomes]
rs35698032	0.82[EUR][1000 genomes]
rs36034295	0.83[EUR][1000 genomes]
rs36093514	0.81[EUR][1000 genomes]
rs41265595	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57857421	0.82[EUR][1000 genomes]
rs6902129	0.82[EUR][1000 genomes]
rs6902374	0.82[EUR][1000 genomes]
rs6902400	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902914	0.82[EUR][1000 genomes]
rs6924512	0.82[EUR][1000 genomes]
rs73727374	0.81[EUR][1000 genomes]
rs9261844	0.82[EUR][1000 genomes]
rs9261893	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9295870	0.82[EUR][1000 genomes]
rs9295872	0.82[EUR][1000 genomes]
rs9295874	0.82[EUR][1000 genomes]
rs9295876	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295885	0.82[EUR][1000 genomes]
rs9295887	0.82[EUR][1000 genomes]
rs9295888	0.82[EUR][1000 genomes]
rs9295889	0.81[EUR][1000 genomes]
rs9295893	0.82[EUR][1000 genomes]
rs9295894	0.82[EUR][1000 genomes]
rs9461608	0.82[EUR][1000 genomes]
rs9461609	0.82[EUR][1000 genomes]
rs9461610	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461611	0.82[EUR][1000 genomes]
rs9468737	0.82[EUR][1000 genomes]
rs9468758	0.82[EUR][1000 genomes]
rs9468759	0.81[EUR][1000 genomes]
rs9468760	0.82[EUR][1000 genomes]
rs9468768	0.82[EUR][1000 genomes]
rs9468771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468773	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9468774	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9501020	0.81[EUR][1000 genomes]
rs9501327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501329	0.82[EUR][1000 genomes]
rs9501335	0.82[EUR][1000 genomes]
rs9501336	0.82[EUR][1000 genomes]
rs9501466	0.82[EUR][1000 genomes]
rs9501468	0.82[EUR][1000 genomes]
rs9501469	0.82[EUR][1000 genomes]
rs9501471	0.82[EUR][1000 genomes]
rs9501472	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501474	0.82[EUR][1000 genomes]
rs9885617	0.82[EUR][1000 genomes]
rs9885618	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9885620	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9885621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885622	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9885815	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9918350	0.82[EUR][1000 genomes]
rs9918389	0.81[EUR][1000 genomes]
rs9918488	0.82[EUR][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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601478	chr6:30383768-30438226	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4959050	C6orf1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30416800-30417800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
2	chr6:30416800-30418000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:30416800-30418200	Bivalent Enhancer	Primary T cells from cord blood	blood

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