Variant report

Variant	rs56119218
Chromosome Location	chr6:26225881-26225882
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:234744354..234747060-chr6:26225401..26227759,2	MCF-7	breast:
2	chr1:149857934..149859702-chr6:26224278..26225955,2	MCF-7	breast:
3	chr15:66160251..66163172-chr6:26224292..26227267,2	MCF-7	breast:
4	chr6:26223757..26226202-chr6:26537228..26539422,2	MCF-7	breast:
5	chr6:26055872..26058402-chr6:26225774..26227439,2	MCF-7	breast:
6	chr6:26030891..26034608-chr6:26223354..26228378,6	MCF-7	breast:
7	chr20:52966595..52969425-chr6:26225517..26227615,2	MCF-7	breast:
8	chr6:26225279..26227416-chr6:27859804..27863883,3	MCF-7	breast:
9	chr6:26225643..26226465-chr6:26234066..26234965,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000103769	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000168264	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11751062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751286	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11751812	0.90[EUR][1000 genomes]
rs11753084	0.86[EUR][1000 genomes]
rs11753717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753837	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11754140	0.90[EUR][1000 genomes]
rs11754368	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757549	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757724	0.88[EUR][1000 genomes]
rs11759758	0.87[EUR][1000 genomes]
rs11760140	0.85[EUR][1000 genomes]
rs16891375	0.87[EUR][1000 genomes]
rs16891407	0.90[EUR][1000 genomes]
rs16891464	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891484	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1981019	0.87[EUR][1000 genomes]
rs2179516	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734534	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs41266811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61746493	0.81[AFR][1000 genomes]
rs61978632	0.82[AFR][1000 genomes]
rs7775052	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv883490	chr6:26172219-26231608	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	316 gene(s)	inside rSNPs	diseases
17	nsv1021294	chr6:26190316-26246784	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	309 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56119218	HIST1H3E	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26223200-26226600	Active TSS	NHLF	lung
2	chr6:26223200-26227000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:26223200-26227400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:26223400-26226000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:26223400-26226000	Active TSS	Brain Germinal Matrix	brain
6	chr6:26223400-26226200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:26223400-26226800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:26223400-26227000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:26223400-26227200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:26223400-26227400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:26223400-26227400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:26223400-26227400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:26223400-26227600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:26223600-26226000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
15	chr6:26223600-26226000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
16	chr6:26223600-26226000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
17	chr6:26223600-26226000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:26223600-26226200	Active TSS	Stomach Mucosa	stomach
19	chr6:26223600-26226400	Active TSS	Colon Smooth Muscle	Colon
20	chr6:26223600-26226400	Bivalent/Poised TSS	NHDF-Ad	bronchial
21	chr6:26223600-26226600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:26223600-26226600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:26223600-26226600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:26223800-26226000	Active TSS	Osteobl	bone
25	chr6:26223800-26226400	Active TSS	Fetal Brain Female	brain
26	chr6:26223800-26226600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:26223800-26226600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:26223800-26226600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:26223800-26226600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:26223800-26226800	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:26223800-26227000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr6:26224000-26226000	Active TSS	Rectal Smooth Muscle	rectum
33	chr6:26224400-26226000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr6:26224600-26226000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:26225000-26226200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:26225200-26226000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:26225200-26226400	ZNF genes & repeats	Liver	Liver
38	chr6:26225200-26226400	Transcr. at gene 5' and 3'	Right Atrium	heart
39	chr6:26225200-26226400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr6:26225200-26226400	ZNF genes & repeats	GM12878-XiMat	blood
41	chr6:26225200-26226400	ZNF genes & repeats	HMEC	breast
42	chr6:26225200-26226400	ZNF genes & repeats	HSMMtube	muscle
43	chr6:26225200-26226600	Flanking Active TSS	Fetal Thymus	thymus
44	chr6:26225400-26226000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:26225400-26226000	ZNF genes & repeats	Thymus	Thymus
46	chr6:26225400-26226000	Flanking Active TSS	NHEK	skin
47	chr6:26225400-26226200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
48	chr6:26225400-26226200	Flanking Active TSS	HUVEC	blood vessel
49	chr6:26225400-26226200	Flanking Active TSS	NH-A	brain
50	chr6:26225400-26226400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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