Variant report

Variant	rs9393831
Chromosome Location	chr6:27588727-27588728
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27588632..27593657-chr6:27594318..27600598,11	K562	blood:
2	chr6:27585919..27588728-chr6:27591058..27593612,2	MCF-7	breast:
3	chr6:27588541..27590422-chr6:27777257..27779773,2	K562	blood:

Variant related genes	Relation type
ENSG00000203813	Chromatin interaction
ENSG00000238648	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1022486	0.93[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs1033451	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807029	0.87[ASN][1000 genomes]
rs10946935	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs10946938	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs10946940	0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs200480	0.81[JPT][hapmap]
rs2056924	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2179096	0.84[ASN][1000 genomes]
rs2294480	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2294481	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713112	0.86[JPT][hapmap]
rs4713113	0.80[EUR][1000 genomes]
rs4713120	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6456799	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6899903	0.86[ASN][1000 genomes]
rs6915266	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs6915987	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs6916878	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs6921256	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6934437	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs6934794	0.93[CEU][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs6936999	0.80[CHD][hapmap]
rs7764081	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs7769662	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295747	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9348772	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9357042	0.90[ASN][1000 genomes]
rs9366697	0.87[ASN][1000 genomes]
rs9380007	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs9393830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][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	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
9	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
10	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
11	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9393831	ZNF391	cis	cerebellum	SCAN
rs9393831	HIST1H2BE	cis	cerebellum	SCAN
rs9393831	HIST1H2AJ	cis	cerebellum	SCAN
rs9393831	HIST1H2BJ	cis	cerebellum	SCAN
rs9393831	ZSCAN23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27586200-27592200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27586800-27591200	Weak transcription	K562	blood
3	chr6:27587800-27592200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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