Variant report

Variant	rs11878341
Chromosome Location	chr19:21698581-21698582
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21691065..21693260-chr19:21696883..21699244,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10426240	1.00[AMR][1000 genomes]
rs11878290	1.00[AMR][1000 genomes]
rs11878313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11878352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11878379	1.00[AMR][1000 genomes]
rs11878890	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11879116	1.00[AMR][1000 genomes]
rs11879186	1.00[AMR][1000 genomes]
rs11880052	1.00[AMR][1000 genomes]
rs11880057	1.00[AMR][1000 genomes]
rs11880270	1.00[AMR][1000 genomes]
rs11880290	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880668	1.00[AMR][1000 genomes]
rs11880717	1.00[AMR][1000 genomes]
rs11882098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11882885	1.00[AMR][1000 genomes]
rs11882927	1.00[AMR][1000 genomes]
rs11883296	1.00[AMR][1000 genomes]
rs1500399	1.00[AMR][1000 genomes]
rs1619077	1.00[AMR][1000 genomes]
rs1678827	1.00[AMR][1000 genomes]
rs1678829	1.00[AMR][1000 genomes]
rs1678830	1.00[AMR][1000 genomes]
rs2013529	1.00[AMR][1000 genomes]
rs2173725	1.00[AMR][1000 genomes]
rs2562418	1.00[AMR][1000 genomes]
rs2562423	1.00[AMR][1000 genomes]
rs2562426	1.00[AMR][1000 genomes]
rs2650761	1.00[AMR][1000 genomes]
rs2650762	1.00[AMR][1000 genomes]
rs2650765	1.00[AMR][1000 genomes]
rs2650795	1.00[AMR][1000 genomes]
rs2650813	1.00[AMR][1000 genomes]
rs28581819	1.00[AMR][1000 genomes]
rs34447812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34475475	1.00[AMR][1000 genomes]
rs34713529	1.00[AMR][1000 genomes]
rs34806732	1.00[AMR][1000 genomes]
rs35147475	1.00[AMR][1000 genomes]
rs35678983	1.00[AMR][1000 genomes]
rs36151394	1.00[AMR][1000 genomes]
rs36168893	1.00[AMR][1000 genomes]
rs6511266	1.00[AMR][1000 genomes]
rs72620584	1.00[AMR][1000 genomes]
rs7343074	1.00[AMR][1000 genomes]
rs7343111	1.00[AMR][1000 genomes]
rs7343124	1.00[AMR][1000 genomes]
rs7343143	1.00[AMR][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	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers 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 target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21689200-21702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21689200-21702000	Weak transcription	Stomach Mucosa	stomach
3	chr19:21689400-21701200	Weak transcription	HSMMtube	muscle
4	chr19:21689400-21701600	Weak transcription	Brain Substantia Nigra	brain
5	chr19:21689400-21701600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:21689400-21702000	Weak transcription	Left Ventricle	heart
7	chr19:21689400-21702000	Weak transcription	Right Ventricle	heart
8	chr19:21689600-21700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:21689600-21701400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:21689600-21701600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:21689600-21702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:21690000-21701400	Weak transcription	Pancreas	Pancrea
13	chr19:21690000-21701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:21690000-21701600	Weak transcription	Osteobl	bone
15	chr19:21690200-21698600	Weak transcription	Fetal Kidney	kidney
16	chr19:21690200-21701600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:21690200-21701600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:21690600-21699600	Weak transcription	Primary T cells from cord blood	blood
19	chr19:21690600-21701600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:21690600-21701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:21691200-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:21691200-21702000	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:21691400-21701200	Weak transcription	Fetal Heart	heart
24	chr19:21691400-21701600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:21691400-21702000	Weak transcription	Ovary	ovary
26	chr19:21691600-21699400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:21691600-21701000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:21692400-21701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:21694600-21701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:21695000-21700600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:21695000-21701400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:21695200-21700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:21695200-21701400	Weak transcription	Thymus	Thymus
34	chr19:21695200-21702000	Weak transcription	Spleen	Spleen
35	chr19:21695400-21700800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:21695400-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:21696800-21701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:21696800-21702000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:21697000-21698600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr19:21697000-21701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:21697000-21701400	Weak transcription	Gastric	stomach
42	chr19:21697000-21702000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:21698000-21702000	Weak transcription	Psoas Muscle	Psoas
44	chr19:21698400-21710800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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