Variant report

Variant	rs12976997
Chromosome Location	chr19:42497555-42497556
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	chr19:42497339-42497590	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr19:42497362-42498650	IMR90	lung:	n/a	chr19:42498042-42498052
3	MAX	chr19:42497484-42498749	A549	lung:	n/a	chr19:42497942-42497952 chr19:42498042-42498052
4	REST	chr19:42497441-42499148	H1-neurons	neurons:	n/a	chr19:42498499-42498508 chr19:42498708-42498721 chr19:42498550-42498563 chr19:42498487-42498501 chr19:42498481-42498501 chr19:42498114-42498127
5	ZNF263	chr19:42497503-42497986	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr19:42497259-42501389	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr19:42497437-42497576	MCF-7	breast:	n/a	n/a
8	USF1	chr19:42497303-42497571	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr19:42497517-42498549	H1-hESC	embryonic stem cell:	n/a	chr19:42498316-42498325
10	MXI1	chr19:42497533-42498255	IMR90	lung:	n/a	n/a
11	BCL3	chr19:42497438-42498162	A549	lung:	n/a	chr19:42498046-42498055 chr19:42498143-42498152 chr19:42498043-42498052
12	POLR2A	chr19:42497361-42499140	H1-neurons	neurons:	n/a	n/a
13	MXI1	chr19:42496312-42499446	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ATP1A3	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10425682	1.00[CHD][hapmap]
rs11083643	1.00[CHD][hapmap]
rs11668239	1.00[CHD][hapmap]
rs12609687	1.00[CHD][hapmap]
rs12985559	1.00[CHD][hapmap]
rs2290694	1.00[CHD][hapmap]
rs34578730	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42495000-42499400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:42495400-42498400	Active TSS	Left Ventricle	heart
3	chr19:42495800-42499000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:42496400-42499200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr19:42496600-42497800	Active TSS	Brain Anterior Caudate	brain
6	chr19:42496600-42498000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:42497000-42497600	Active TSS	Right Atrium	heart
8	chr19:42497000-42498200	Active TSS	Fetal Heart	heart
9	chr19:42497200-42497600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:42497200-42497600	Active TSS	Right Ventricle	heart
11	chr19:42497200-42498000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:42497400-42497600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:42497400-42497600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
14	chr19:42497400-42497600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
15	chr19:42497400-42497600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:42497400-42497600	Enhancers	Primary B cells from cord blood	blood
17	chr19:42497400-42497600	Enhancers	Primary T cells from cord blood	blood
18	chr19:42497400-42497600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
19	chr19:42497400-42497600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:42497400-42497600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:42497400-42497600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:42497400-42497600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:42497400-42497600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:42497400-42497600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:42497400-42497600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:42497400-42497600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:42497400-42497600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr19:42497400-42497600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:42497400-42497600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:42497400-42497600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
31	chr19:42497400-42497600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr19:42497400-42497600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
33	chr19:42497400-42497600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
34	chr19:42497400-42497600	Bivalent Enhancer	Fetal Thymus	thymus
35	chr19:42497400-42497600	Active TSS	Thymus	Thymus
36	chr19:42497400-42497600	Enhancers	Spleen	Spleen
37	chr19:42497400-42497800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
38	chr19:42497400-42497800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr19:42497400-42497800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
40	chr19:42497400-42497800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:42497400-42497800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:42497400-42497800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:42497400-42497800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr19:42497400-42497800	Enhancers	Gastric	stomach
45	chr19:42497400-42497800	Enhancers	Pancreas	Pancrea
46	chr19:42497400-42497800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr19:42497400-42497800	Bivalent Enhancer	A549	lung
48	chr19:42497400-42498000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
49	chr19:42497400-42498000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:42497400-42498000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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