Variant report

Variant	rs12461721
Chromosome Location	chr19:37127148-37127149
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	chr19:37125356..37128254-chr19:37129692..37132005,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF461-3	chr19:37127121-37127181	l_1675_chr19:37069368-37128185_testes

Variant related genes	Relation type
ENSG00000197808	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

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]
rs1227559	1.00[ASN][1000 genomes]
rs1227561	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]
rs12459377	1.00[AFR][1000 genomes];0.90[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]
rs12459894	1.00[AFR][1000 genomes];0.90[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]
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]
rs12461970	1.00[AFR][1000 genomes];1.00[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]
rs12463012	0.90[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]
rs1625762	1.00[ASN][1000 genomes]
rs1673083	1.00[ASN][1000 genomes]
rs16971568	1.00[ASN][1000 genomes]
rs16973489	1.00[ASN][1000 genomes]
rs17468285	1.00[ASN][1000 genomes]
rs1990964	1.00[AFR][1000 genomes];0.90[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]
rs3859520	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs491951	0.90[ASN][1000 genomes]
rs500244	0.90[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:9 , 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	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
3	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
5	chr19:37107000-37134800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37107800-37134600	ZNF genes & repeats	Brain Anterior Caudate	brain
8	chr19:37110400-37152600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:37115400-37131800	ZNF genes & repeats	Left Ventricle	heart
10	chr19:37117800-37128400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37121400-37127600	ZNF genes & repeats	Brain Angular Gyrus	brain
12	chr19:37121400-37134600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr19:37121600-37135200	ZNF genes & repeats	Brain Hippocampus Middle	brain
14	chr19:37122000-37127800	ZNF genes & repeats	Fetal Brain Male	brain
15	chr19:37122600-37139800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
16	chr19:37122800-37134800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:37124600-37134600	ZNF genes & repeats	Brain Substantia Nigra	brain
18	chr19:37124800-37155600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:37125000-37128000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:37125000-37128000	ZNF genes & repeats	Fetal Lung	lung
21	chr19:37125000-37134600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
22	chr19:37125000-37134600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr19:37125800-37127200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:37126000-37128400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
25	chr19:37126000-37134600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr19:37126200-37128000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
27	chr19:37126200-37134600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
28	chr19:37126200-37156200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:37126400-37136200	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr19:37127000-37128600	ZNF genes & repeats	Lung	lung
31	chr19:37127000-37129800	ZNF genes & repeats	Fetal Stomach	stomach
32	chr19:37127000-37134400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr19:37127000-37140000	ZNF genes & repeats	Ovary	ovary

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