Variant report

Variant	rs9379827
Chromosome Location	chr6:26153335-26153336
allele	A/C
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	MYC	chr6:26152455-26153345	MCF10A-Er-Src	breast:	n/a	chr6:26153019-26153028 chr6:26153213-26153222 chr6:26153020-26153029
2	GATA3	chr6:26152709-26153524	SK-N-SH	brain:	n/a	n/a
3	FOS	chr6:26152454-26153346	MCF10A-Er-Src	breast:	n/a	chr6:26153021-26153032 chr6:26153020-26153027 chr6:26153019-26153028 chr6:26153018-26153030 chr6:26153019-26153029 chr6:26153020-26153028
4	USF1	chr6:26153021-26153370	SK-N-SH_RA	brain:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
5	BHLHE40	chr6:26153033-26153385	K562	blood:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
6	FOSL2	chr6:26152717-26153337	SK-N-SH	brain:	n/a	chr6:26153021-26153032 chr6:26153020-26153027 chr6:26153019-26153028 chr6:26153018-26153030 chr6:26153019-26153029 chr6:26153020-26153028
7	USF1	chr6:26153074-26153339	SK-N-SH_RA	brain:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
8	SP1	chr6:26152677-26153459	HCT-116	colon:	n/a	n/a
9	NFYB	chr6:26153067-26153375	K562	blood:	n/a	chr6:26153237-26153252
10	USF1	chr6:26153087-26153345	A549	lung:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
11	CEBPB	chr6:26153179-26153376	A549	lung:	n/a	chr6:26153269-26153280
12	NFYB	chr6:26153062-26153361	Hela-S3	cervix:	n/a	chr6:26153237-26153252
13	USF1	chr6:26152969-26153340	K562	blood:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
14	GATA3	chr6:26152724-26153489	SK-N-SH	brain:	n/a	n/a
15	CEBPB	chr6:26153131-26153353	Hela-S3	cervix:	n/a	chr6:26153269-26153280
16	FOS	chr6:26152480-26153346	MCF10A-Er-Src	breast:	n/a	chr6:26153021-26153032 chr6:26153020-26153027 chr6:26153019-26153028 chr6:26153018-26153030 chr6:26153019-26153029 chr6:26153020-26153028
17	USF2	chr6:26153059-26153365	Hela-S3	cervix:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153223 chr6:26153212-26153221
18	USF1	chr6:26153016-26153361	SK-N-SH	brain:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221
19	FOSL1	chr6:26152766-26153358	HCT-116	colon:	n/a	chr6:26153021-26153032 chr6:26153020-26153027 chr6:26153019-26153028 chr6:26153018-26153030 chr6:26153019-26153029 chr6:26153020-26153028
20	USF1	chr6:26152927-26153477	HCT-116	colon:	n/a	chr6:26153207-26153228 chr6:26153211-26153224 chr6:26153213-26153222 chr6:26153214-26153223 chr6:26153213-26153222 chr6:26153212-26153221

No.	Distal block	Cell Line	Cell type
1	chr6:26051079..26061905-chr6:26152751..26161537,32	MCF-7	breast:
2	chr6:26151480..26154019-chr6:27100523..27102546,2	K562	blood:
3	chr6:26032541..26034170-chr6:26151857..26154008,2	MCF-7	breast:
4	chr6:26151788..26154019-chr6:27100138..27102546,2	K562	blood:

Variant related genes	Relation type
HIST1H1E	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1009181	0.89[CHD][hapmap]
rs10484437	0.85[MKK][hapmap]
rs1341758	0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs16891417	0.96[MKK][hapmap]
rs16891512	0.91[MKK][hapmap]
rs16891517	0.91[MKK][hapmap]
rs16891518	0.91[MKK][hapmap]
rs17533076	0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs17600910	0.91[MKK][hapmap]
rs2066295	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2183947	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34550794	0.96[MKK][hapmap];1.00[YRI][hapmap]
rs4486004	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4593350	1.00[YRI][hapmap]
rs72834694	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72834696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7450543	0.91[MKK][hapmap]
rs806973	0.89[CHD][hapmap]
rs9358909	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9366639	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9379829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379831	0.86[CHD][hapmap]
rs989710	0.96[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	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
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	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
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	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
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	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
17	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
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
19	nsv518431	chr6:26148311-26211368	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
20	nsv526456	chr6:26148311-26211368	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9379827	HIST1H2BD	cis	multi-tissue	Pritchard
rs9379827	HIST1H4H	cis	parietal	SCAN
rs9379827	TBC1D30	trans	lymphoblastoid	seeQTL
rs9379827	HIST1H3H	cis	parietal	SCAN
rs9379827	ZSCAN23	cis	cerebellum	SCAN
rs9379827	HIST1H2BJ	cis	cerebellum	SCAN
rs9379827	HIST1H1C	cis	parietal	SCAN
rs9379827	SCGN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26130600-26155600	Weak transcription	Right Atrium	heart
2	chr6:26131600-26156000	Weak transcription	Esophagus	oesophagus
3	chr6:26132000-26155200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:26139600-26155600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:26140000-26155400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:26140800-26155600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:26140800-26155600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:26141000-26155800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:26141200-26155200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:26141200-26155400	Weak transcription	Fetal Thymus	thymus
11	chr6:26141200-26155400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:26141200-26155800	Weak transcription	Placenta	Placenta
13	chr6:26142600-26156000	Weak transcription	Left Ventricle	heart
14	chr6:26143200-26155200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:26144200-26155400	Weak transcription	Primary B cells from cord blood	blood
16	chr6:26148200-26155600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:26151400-26153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:26152000-26153400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:26152200-26153400	Enhancers	A549	lung
20	chr6:26152400-26154000	Enhancers	HMEC	breast
21	chr6:26152600-26153400	Enhancers	Hela-S3	cervix
22	chr6:26152600-26153400	Enhancers	HepG2	liver
23	chr6:26152600-26153800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:26152800-26153400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:26152800-26153400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:26152800-26153400	Enhancers	K562	blood
27	chr6:26152800-26153600	Flanking Active TSS	NHEK	skin
28	chr6:26153200-26153400	Enhancers	NH-A	brain
29	chr6:26153200-26153800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:26153200-26155400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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