Variant report

Variant	rs62122972
Chromosome Location	chr19:23301329-23301330
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:23256417..23259218-chr19:23299816..23301387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183850	Chromatin interaction
ENSG00000267886	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10413951	0.82[ASN][1000 genomes]
rs10416036	0.89[ASN][1000 genomes]
rs10424321	0.89[ASN][1000 genomes]
rs10460208	0.92[ASN][1000 genomes]
rs11668065	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11668225	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668373	0.89[ASN][1000 genomes]
rs11668895	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11669996	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11670477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671123	0.89[ASN][1000 genomes]
rs11671676	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11672544	0.89[ASN][1000 genomes]
rs11672552	0.89[ASN][1000 genomes]
rs11672593	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11672720	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11672966	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16999783	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2362140	0.89[ASN][1000 genomes]
rs34402206	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62121611	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62121613	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62121615	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62121616	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62122966	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62122968	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62122969	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62122970	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62122971	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122978	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122981	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507929	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription 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	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv1058070	chr19:22994261-23315207	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
6	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
7	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
8	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
10	esv3424935	chr19:23111817-23495542	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
11	esv3504832	chr19:23114495-23397124	Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv3504833	chr19:23114495-23397124	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv469842	chr19:23164234-23322414	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv482669	chr19:23164234-23322414	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv932212	chr19:23170413-23372286	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	esv3413015	chr19:23172466-23416111	Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv833788	chr19:23179045-23328665	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	esv3334703	chr19:23235234-23310623	Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
20	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
21	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
22	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS 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	47 gene(s)	inside rSNPs	diseases
23	nsv1060295	chr19:23276069-23382990	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1061493	chr19:23289066-23419445	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv963133	chr19:23290648-23328122	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv911458	chr19:23297503-23353024	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23299400-23301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:23299400-23301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:23299400-23301800	Active TSS	Fetal Brain Female	brain
4	chr19:23299800-23301600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:23299800-23301800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:23300400-23301600	Flanking Active TSS	Dnd41	blood
7	chr19:23300400-23306800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:23300600-23301400	Flanking Active TSS	Fetal Brain Male	brain
9	chr19:23300600-23301400	Enhancers	Fetal Heart	heart
10	chr19:23300600-23303400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:23300600-23304000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:23300600-23306600	Weak transcription	Ovary	ovary
13	chr19:23300600-23306800	Weak transcription	Thymus	Thymus
14	chr19:23300600-23310400	Weak transcription	Right Atrium	heart
15	chr19:23300800-23301400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr19:23300800-23301400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:23300800-23301600	Enhancers	Fetal Stomach	stomach
18	chr19:23300800-23301800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr19:23300800-23302000	Enhancers	Fetal Lung	lung
20	chr19:23300800-23306200	Weak transcription	Primary B cells from cord blood	blood
21	chr19:23301000-23301400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:23301000-23301600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:23301000-23301600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:23301000-23301800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:23301000-23303000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:23301000-23304200	Weak transcription	HSMM	muscle
27	chr19:23301000-23305000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:23301000-23305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:23301000-23306800	Weak transcription	NH-A	brain
30	chr19:23301000-23310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:23301000-23310600	Weak transcription	Fetal Kidney	kidney
32	chr19:23301000-23310800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:23301200-23301400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:23301200-23301400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr19:23301200-23301400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:23301200-23301400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr19:23301200-23301400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:23301200-23301600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:23301200-23301600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:23301200-23301600	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr19:23301200-23301600	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr19:23301200-23302000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:23301200-23302000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:23301200-23302000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr19:23301200-23302000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:23301200-23302200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr19:23301200-23304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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