Variant report

Variant	rs12461970
Chromosome Location	chr19:37058701-37058702
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	chr19:37057613..37059554-chr19:37062678..37064206,2	MCF-7	breast:
2	chr19:37057331..37060985-chr19:37062478..37065341,6	K562	blood:

Variant related genes	Relation type
ENSG00000186020	Chromatin interaction
ENSG00000233527	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10408063	1.00[ASN][1000 genomes]
rs10410939	1.00[ASN][1000 genomes]
rs10411150	0.90[ASN][1000 genomes]
rs10413876	1.00[ASN][1000 genomes]
rs10414240	1.00[ASN][1000 genomes]
rs10418271	1.00[ASN][1000 genomes]
rs11880022	1.00[ASN][1000 genomes]
rs11880159	1.00[ASN][1000 genomes]
rs12459208	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12459218	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12459243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459325	1.00[ASN][1000 genomes]
rs12459429	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459527	1.00[ASN][1000 genomes]
rs12459808	1.00[ASN][1000 genomes]
rs12459915	1.00[ASN][1000 genomes]
rs12459923	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460354	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460418	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460420	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460455	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460482	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460774	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461023	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461264	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461265	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461280	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461738	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461954	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462037	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462268	1.00[ASN][1000 genomes]
rs12462281	1.00[ASN][1000 genomes]
rs12462325	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462454	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462471	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12462635	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16971568	1.00[ASN][1000 genomes]
rs16973489	1.00[ASN][1000 genomes]
rs17468285	1.00[ASN][1000 genomes]
rs25419	1.00[ASN][1000 genomes]
rs28398875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28465595	1.00[ASN][1000 genomes]
rs28472526	1.00[ASN][1000 genomes]
rs28645577	1.00[ASN][1000 genomes]
rs28742010	1.00[ASN][1000 genomes]
rs28818888	1.00[ASN][1000 genomes]
rs34051375	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34106502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35621405	1.00[ASN][1000 genomes]
rs35706444	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58245911	1.00[ASN][1000 genomes]
rs60268308	1.00[ASN][1000 genomes]
rs60615280	1.00[ASN][1000 genomes]
rs61750934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6510562	1.00[ASN][1000 genomes]
rs73609133	1.00[ASN][1000 genomes]
rs73612031	1.00[ASN][1000 genomes]
rs73612043	1.00[ASN][1000 genomes]
rs73615692	1.00[ASN][1000 genomes]
rs73615693	0.90[ASN][1000 genomes]
rs7508258	1.00[ASN][1000 genomes]
rs8104355	0.90[ASN][1000 genomes]
rs8111419	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
2	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
7	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:37025600-37061000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:37025800-37060200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
14	chr19:37028600-37061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr19:37029000-37060000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
16	chr19:37034000-37063000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:37034200-37059600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
18	chr19:37036200-37059400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:37047000-37058800	Weak transcription	K562	blood
20	chr19:37048400-37062800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:37049800-37061800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:37050400-37062600	Weak transcription	Fetal Heart	heart
23	chr19:37051400-37060800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:37052800-37059600	Weak transcription	HSMMtube	muscle
25	chr19:37052800-37063000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:37052800-37063200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:37053400-37060800	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr19:37053400-37063000	Weak transcription	Stomach Mucosa	stomach
29	chr19:37054000-37059800	Weak transcription	Hela-S3	cervix
30	chr19:37054000-37059800	Weak transcription	NH-A	brain
31	chr19:37054000-37063200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:37054200-37063000	Weak transcription	Osteobl	bone
33	chr19:37054200-37063800	Weak transcription	Gastric	stomach
34	chr19:37054400-37060800	Weak transcription	Pancreas	Pancrea
35	chr19:37054400-37063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:37055200-37059600	Weak transcription	Fetal Kidney	kidney
37	chr19:37055200-37061600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
38	chr19:37055400-37061600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:37055600-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:37055600-37062000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:37055600-37062800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:37055600-37063000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr19:37055800-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:37056000-37060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:37056000-37063400	ZNF genes & repeats	A549	lung
46	chr19:37056200-37058800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:37056200-37059200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr19:37056200-37059200	Weak transcription	Brain Anterior Caudate	brain
49	chr19:37056200-37061600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:37056200-37061600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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