Variant report

Variant	rs9461392
Chromosome Location	chr6:27566169-27566170
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	chr6:27519259..27522990-chr6:27565885..27571122,5	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1028311	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10946943	0.93[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1157432	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12055685	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs16867916	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16867976	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs16867983	0.93[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2142704	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2143082	0.81[EUR][1000 genomes]
rs4236044	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711157	0.90[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713114	0.89[EUR][1000 genomes]
rs4713119	1.00[LWK][hapmap]
rs6456790	1.00[YRI][hapmap]
rs6456798	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906653	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6908024	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6911283	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6920044	0.93[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs6934295	0.90[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6936653	0.84[ASN][1000 genomes]
rs73739763	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7763685	0.90[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9348777	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs9357044	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9357048	0.93[CHB][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs9368524	0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs9379994	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379995	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380001	0.93[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs9393826	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393832	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393835	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393836	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393838	0.90[EUR][1000 genomes]
rs9393839	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461389	0.84[EUR][1000 genomes]
rs9468157	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468158	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs970668	0.90[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9461392	ZSCAN23	cis	cerebellum	SCAN
rs9461392	HIST1H2BE	cis	cerebellum	SCAN
rs9461392	ZNF391	cis	cerebellum	SCAN
rs9461392	HIST1H2BJ	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27562200-27567600	Weak transcription	GM12878-XiMat	blood
2	chr6:27563000-27568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27563200-27567800	Weak transcription	K562	blood
4	chr6:27565600-27567800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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