Variant report

Variant	rs4133107
Chromosome Location	chr19:55954463-55954464
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	SUZ12	chr19:55952383-55955792	NT2-D1	testis:	n/a	n/a
2	POLR2A	chr19:55954451-55955086	H1-neurons	neurons:	n/a	n/a
3	E2F6	chr19:55953299-55954845	H1-hESC	embryonic stem cell:	n/a	chr19:55954296-55954308 chr19:55954363-55954372 chr19:55953534-55953545
4	E2F6	chr19:55954315-55954702	K562	blood:	n/a	chr19:55954363-55954372
5	POLR2A	chr19:55954424-55954706	H1-neurons	neurons:	n/a	n/a
6	EGR1	chr19:55954352-55954807	K562	blood:	n/a	chr19:55954358-55954368 chr19:55954365-55954378 chr19:55954362-55954372
7	MAX	chr19:55954367-55954903	H1-hESC	embryonic stem cell:	n/a	chr19:55954453-55954462

No.	Distal block	Cell Line	Cell type
1	chr19:55897252..55900237-chr19:55952546..55954535,2	K562	blood:
2	chr19:55917609..55921205-chr19:55953986..55957164,3	MCF-7	breast:
3	chr19:55953960..55955842-chr19:55970927..55973653,2	MCF-7	breast:
4	chr19:55917160..55920807-chr19:55952217..55954554,6	K562	blood:
5	chr19:55896562..55898629-chr19:55953119..55955892,2	MCF-7	breast:
6	chr19:55917160..55921382-chr19:55952217..55958073,12	K562	blood:
7	chr19:55910844..55913006-chr19:55952542..55954951,2	K562	blood:

Variant related genes	Relation type
SHISA7	TF binding region
ENSG00000267093	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000108106	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11668893	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531215	0.87[JPT][hapmap]
rs2384684	0.86[JPT][hapmap]
rs4075908	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4801608	0.88[CEU][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72489180	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv912477	chr19:55936376-55972950	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv912478	chr19:55936376-56045522	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv912479	chr19:55942456-55969746	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv3376613	chr19:55952665-55955513	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
9	esv3422614	chr19:55952890-55955638	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55951600-55955200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr19:55951600-55955200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr19:55951800-55954800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:55951800-55955000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr19:55952000-55954600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:55952000-55954800	Bivalent Enhancer	Fetal Stomach	stomach
7	chr19:55952000-55955200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
8	chr19:55952200-55955400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:55952600-55954800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:55952800-55955000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:55952800-55955600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr19:55953200-55954600	Bivalent Enhancer	Lung	lung
13	chr19:55953400-55954800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:55953400-55955000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr19:55953400-55955000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr19:55953400-55955200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr19:55953400-55956400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:55953600-55954600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
19	chr19:55953600-55954600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:55953600-55954600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:55953600-55954800	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:55953600-55954800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr19:55953600-55955000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr19:55953600-55955000	Active TSS	Brain Anterior Caudate	brain
25	chr19:55953600-55955000	Active TSS	Brain Cingulate Gyrus	brain
26	chr19:55953600-55955000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr19:55953600-55955200	Bivalent Enhancer	Spleen	Spleen
28	chr19:55954000-55954600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr19:55954200-55954600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr19:55954200-55954600	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr19:55954200-55954600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
32	chr19:55954200-55954800	Bivalent/Poised TSS	Thymus	Thymus
33	chr19:55954200-55955400	Bivalent Enhancer	Fetal Brain Male	brain
34	chr19:55954200-55962800	Weak transcription	Right Atrium	heart
35	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
37	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:55954400-55954600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:55954400-55954600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:55954400-55954600	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
44	chr19:55954400-55954600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
45	chr19:55954400-55954600	Bivalent Enhancer	Esophagus	oesophagus
46	chr19:55954400-55954600	Bivalent Enhancer	Placenta	Placenta
47	chr19:55954400-55954600	Bivalent Enhancer	Dnd41	blood
48	chr19:55954400-55954600	Bivalent/Poised TSS	HSMM	muscle
49	chr19:55954400-55954600	Flanking Active TSS	K562	blood
50	chr19:55954400-55954800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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