Variant report

Variant	rs3778279
Chromosome Location	chr6:26325463-26325464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:26321218-26326187	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26250927..26253821-chr6:26323382..26326014,4	MCF-7	breast:
2	chr6:26323417..26326776-chr6:26326785..26329865,3	MCF-7	breast:
3	chr6:26270322..26272266-chr6:26323599..26325773,2	MCF-7	breast:
4	chr6:26324380..26326185-chr6:26473831..26475753,2	K562	blood:
5	chr6:26322866..26325773-chr6:26327005..26329096,3	MCF-7	breast:
6	chr6:26323439..26325517-chr6:27099019..27100610,2	K562	blood:
7	chr6:26325462..26328933-chr6:26567431..26570210,5	K562	blood:

No data

Variant related genes	Relation type
HIST1H3PS1	TF binding region
ENSG00000256018	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1053860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946810	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11751978	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs11752014	0.83[JPT][hapmap];0.81[YRI][hapmap]
rs12660432	0.88[ASN][1000 genomes]
rs12665035	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13210340	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16891523	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs16891525	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs17608582	0.88[ASN][1000 genomes]
rs1883213	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1883214	0.83[JPT][hapmap];0.82[YRI][hapmap]
rs1987244	0.84[ASN][1000 genomes]
rs2893820	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2893842	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2893843	0.83[JPT][hapmap]
rs4412193	0.83[JPT][hapmap]
rs4631273	0.83[JPT][hapmap]
rs61324092	0.84[ASN][1000 genomes]
rs62394764	0.84[ASN][1000 genomes]
rs62394768	0.90[ASN][1000 genomes]
rs62394769	0.83[ASN][1000 genomes]
rs6456713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914596	0.83[JPT][hapmap]
rs6917995	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6918325	0.90[ASN][1000 genomes]
rs6930616	0.83[JPT][hapmap]
rs6932584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725575	0.84[ASN][1000 genomes]
rs7755741	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs9358914	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9358918	0.83[JPT][hapmap]
rs9358924	0.81[ASN][1000 genomes]
rs9358925	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9358926	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9358927	0.83[JPT][hapmap]
rs9366648	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9379842	0.92[JPT][hapmap]
rs9379846	0.86[ASN][1000 genomes]
rs9393691	0.92[JPT][hapmap]
rs9393700	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs994379	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3778279	HIST1H3E	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26322800-26327200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:26322800-26327400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:26322800-26327400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:26322800-26327400	Weak transcription	NHLF	lung
5	chr6:26322800-26331200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:26323000-26326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:26323000-26326800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:26323000-26327600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:26323400-26327000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:26323400-26327200	Weak transcription	Placenta	Placenta
11	chr6:26323400-26327200	Weak transcription	HMEC	breast
12	chr6:26323400-26327600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:26323600-26326600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:26323600-26326800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:26323600-26326800	Weak transcription	GM12878-XiMat	blood
16	chr6:26323600-26327000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:26323600-26327000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:26323600-26327200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:26323600-26327200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:26323600-26327400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:26323600-26327400	Weak transcription	NH-A	brain
22	chr6:26323600-26327600	Weak transcription	Dnd41	blood
23	chr6:26323600-26327600	Weak transcription	NHDF-Ad	bronchial
24	chr6:26323600-26327800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:26323600-26327800	Weak transcription	HSMM	muscle
26	chr6:26323800-26326600	Weak transcription	A549	lung
27	chr6:26323800-26326800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:26323800-26327200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:26324200-26326600	Enhancers	K562	blood
30	chr6:26325000-26326200	Enhancers	HepG2	liver

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