Variant report

Variant	rs12976751
Chromosome Location	chr19:52874293-52874294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10423030	0.87[ASN][1000 genomes]
rs12976033	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs12978149	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12983120	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162116	0.82[LWK][hapmap]
rs34830840	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35280531	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35721330	0.90[EUR][1000 genomes]
rs35752205	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35953943	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36009530	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56374938	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs707312	0.82[LWK][hapmap]
rs73934445	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic 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	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
3	chr19:52871200-52876400	Weak transcription	Dnd41	blood
4	chr19:52872600-52874400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:52872600-52874400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:52872600-52874400	Active TSS	Fetal Kidney	kidney
7	chr19:52872600-52874800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:52872800-52874400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:52872800-52874400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:52872800-52874400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr19:52872800-52874400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:52872800-52874400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:52872800-52874400	Active TSS	NH-A	brain
14	chr19:52872800-52874400	Active TSS	NHDF-Ad	bronchial
15	chr19:52872800-52874600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:52872800-52874600	ZNF genes & repeats	GM12878-XiMat	blood
17	chr19:52872800-52875000	ZNF genes & repeats	Fetal Thymus	thymus
18	chr19:52872800-52875200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:52872800-52875200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
20	chr19:52872800-52875400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:52873200-52875200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:52873400-52874400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:52873400-52875400	ZNF genes & repeats	Placenta	Placenta
24	chr19:52873600-52874400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
25	chr19:52873600-52874400	Flanking Active TSS	Fetal Brain Male	brain
26	chr19:52873600-52874600	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr19:52873600-52874800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr19:52873600-52875200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:52873600-52888400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr19:52873800-52875200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr19:52873800-52877600	Weak transcription	Aorta	Aorta
32	chr19:52873800-52877600	Weak transcription	Gastric	stomach
33	chr19:52873800-52885000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr19:52874000-52874400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:52874000-52874400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:52874000-52874400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr19:52874000-52874400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr19:52874000-52874400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr19:52874000-52874400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr19:52874000-52874400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr19:52874000-52874400	Transcr. at gene 5' and 3'	HSMMtube	muscle
42	chr19:52874000-52874600	Flanking Active TSS	Fetal Heart	heart
43	chr19:52874000-52874800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:52874000-52875000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr19:52874000-52875000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:52874000-52875200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:52874000-52875200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:52874000-52875200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr19:52874000-52875200	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr19:52874000-52875400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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