Variant report

Variant	rs12459923
Chromosome Location	chr19:37071379-37071380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:65596793..65597620-chr19:37071052..37071553,2	MCF-7	breast:
2	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
3	chr19:37062757..37066475-chr19:37067178..37075829,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF529-2	chr19:37071155-37073606	NONHSAT066017

Variant related genes	Relation type
ENSG00000200156	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000186020	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

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[ASN][1000 genomes]
rs12459218	1.00[ASN][1000 genomes]
rs12459243	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459325	1.00[ASN][1000 genomes]
rs12459429	1.00[ASN][1000 genomes]
rs12459527	1.00[ASN][1000 genomes]
rs12459808	1.00[ASN][1000 genomes]
rs12459915	1.00[ASN][1000 genomes]
rs12460049	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460354	1.00[ASN][1000 genomes]
rs12460418	1.00[ASN][1000 genomes]
rs12460420	1.00[ASN][1000 genomes]
rs12460430	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460455	1.00[ASN][1000 genomes]
rs12460482	1.00[ASN][1000 genomes]
rs12460729	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460774	1.00[ASN][1000 genomes]
rs12461023	1.00[ASN][1000 genomes]
rs12461264	1.00[ASN][1000 genomes]
rs12461265	1.00[ASN][1000 genomes]
rs12461280	1.00[ASN][1000 genomes]
rs12461436	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461474	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461707	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461721	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461723	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461738	1.00[ASN][1000 genomes]
rs12461954	1.00[ASN][1000 genomes]
rs12461970	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462037	1.00[ASN][1000 genomes]
rs12462268	1.00[ASN][1000 genomes]
rs12462281	1.00[ASN][1000 genomes]
rs12462325	1.00[ASN][1000 genomes]
rs12462454	1.00[ASN][1000 genomes]
rs12462471	0.90[ASN][1000 genomes]
rs12462635	1.00[ASN][1000 genomes]
rs12462921	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974130	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974446	0.88[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]
rs25419	1.00[ASN][1000 genomes]
rs28398875	0.88[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[ASN][1000 genomes]
rs34106502	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35621405	1.00[ASN][1000 genomes]
rs35706444	1.00[ASN][1000 genomes]
rs58245911	1.00[ASN][1000 genomes]
rs60268308	1.00[ASN][1000 genomes]
rs60615280	1.00[ASN][1000 genomes]
rs61750934	0.88[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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37065600-37081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37065600-37095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:37065800-37072000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:37065800-37072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:37065800-37075200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:37065800-37076600	Weak transcription	Stomach Mucosa	stomach
7	chr19:37065800-37078200	Weak transcription	Right Ventricle	heart
8	chr19:37066000-37081200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:37066000-37081200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37066200-37071400	Weak transcription	HepG2	liver
11	chr19:37066200-37073200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:37066600-37072000	Strong transcription	HUVEC	blood vessel
13	chr19:37066600-37073200	Strong transcription	Fetal Muscle Leg	muscle
14	chr19:37066600-37073400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr19:37066600-37073400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:37066600-37073400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr19:37066600-37074200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:37066600-37074200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr19:37066600-37080600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:37066800-37074400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:37066800-37081000	Strong transcription	Dnd41	blood
22	chr19:37066800-37091400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:37067000-37072200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:37067000-37073200	Strong transcription	Placenta	Placenta
25	chr19:37067000-37073800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:37067000-37076200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:37067000-37076800	ZNF genes & repeats	GM12878-XiMat	blood
28	chr19:37067000-37080800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:37067000-37081200	ZNF genes & repeats	Liver	Liver
30	chr19:37067000-37081200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
31	chr19:37067200-37072000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:37067200-37072000	Strong transcription	HSMM	muscle
33	chr19:37067400-37072800	Strong transcription	Fetal Thymus	thymus
34	chr19:37067400-37074600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr19:37067600-37072200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:37067800-37072000	Strong transcription	Fetal Brain Female	brain
37	chr19:37067800-37072600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:37067800-37072800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:37067800-37074600	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr19:37068000-37071800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:37068000-37071800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:37068000-37072400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:37068000-37072400	Strong transcription	Osteobl	bone
44	chr19:37068000-37072600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:37068000-37072600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:37068000-37072600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:37068000-37072600	Strong transcription	Fetal Kidney	kidney
48	chr19:37068000-37072800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
49	chr19:37068000-37073200	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr19:37068000-37074000	Strong transcription	Left Ventricle	heart

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