Variant report

Variant	rs9379842
Chromosome Location	chr6:26289310-26289311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:26289039-26289547	K562	blood:	n/a	n/a
2	KAP1	chr6:26288006-26289333	K562	blood:	n/a	n/a
3	SETDB1	chr6:26287877-26290394	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
2	chr6:26283501..26289776-chr6:27108470..27116413,14	K562	blood:

Variant related genes	Relation type
HIST1H4H	TF binding region
ENSG00000217862	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1053860	0.92[JPT][hapmap]
rs10946808	0.82[JPT][hapmap]
rs10946810	0.81[CEU][hapmap];0.92[JPT][hapmap]
rs11755943	0.82[JPT][hapmap]
rs11759682	0.82[JPT][hapmap]
rs11759720	0.82[JPT][hapmap]
rs12525187	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12660432	0.81[EUR][1000 genomes]
rs12661552	0.81[EUR][1000 genomes]
rs12665035	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs17608582	0.81[EUR][1000 genomes]
rs1883213	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1987244	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1997768	0.82[JPT][hapmap]
rs2893820	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2893842	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2893843	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734533	0.82[JPT][hapmap]
rs3778279	0.92[JPT][hapmap]
rs3823157	0.82[JPT][hapmap]
rs4412192	0.81[GIH][hapmap]
rs4412193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61324092	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394764	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394768	0.82[EUR][1000 genomes]
rs6901243	0.82[JPT][hapmap]
rs6908402	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6916289	0.81[GIH][hapmap]
rs6917995	0.82[ASN][1000 genomes]
rs6918325	0.81[EUR][1000 genomes]
rs6930616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932584	0.89[JPT][hapmap]
rs725575	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755741	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs811041	0.82[JPT][hapmap]
rs9357005	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9358913	0.82[JPT][hapmap]
rs9358914	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs9358916	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358918	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358925	0.92[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs9358926	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9358927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366648	0.88[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9366650	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379846	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393693	1.00[YRI][hapmap]
rs9393696	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393697	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs994379	0.80[GIH][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
8	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
9	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
10	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9379842	MRS2	cis	parietal	SCAN
rs9379842	WDR90	trans	parietal	SCAN
rs9379842	HIST1H3C	cis	parietal	SCAN
rs9379842	ACOT13	cis	cerebellum	SCAN
rs9379842	HIST1H4H	cis	cerebellum	SCAN
rs9379842	HIST1H2BD	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26286800-26290400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:26286800-26292200	Weak transcription	Ovary	ovary
3	chr6:26286800-26294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:26286800-26295400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:26287000-26291600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:26287200-26294400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:26287200-26295600	Weak transcription	A549	lung
8	chr6:26287800-26289400	ZNF genes & repeats	Dnd41	blood
9	chr6:26289000-26294400	Weak transcription	K562	blood

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