Variant report

Variant	rs12462454
Chromosome Location	chr19:37294666-37294667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37270866..37273787-chr19:37294233..37296102,2	MCF-7	breast:
2	chr19:37290133..37291956-chr19:37293759..37296212,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10408063	1.00[ASN][1000 genomes]
rs10410939	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10411150	0.90[ASN][1000 genomes]
rs10413876	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10414240	1.00[ASN][1000 genomes]
rs10418271	1.00[ASN][1000 genomes]
rs1114318	0.94[AMR][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[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459243	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12459325	1.00[ASN][1000 genomes]
rs12459377	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12459429	1.00[ASN][1000 genomes]
rs12459527	1.00[ASN][1000 genomes]
rs12459808	1.00[ASN][1000 genomes]
rs12459894	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12459915	1.00[ASN][1000 genomes]
rs12459923	1.00[ASN][1000 genomes]
rs12460049	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460354	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460430	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460455	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460482	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460729	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460774	1.00[ASN][1000 genomes]
rs12461023	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461264	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461436	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461474	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461707	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461721	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461723	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461954	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461970	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462151	0.82[AMR][1000 genomes]
rs12462268	1.00[ASN][1000 genomes]
rs12462281	1.00[ASN][1000 genomes]
rs12462325	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12462635	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462921	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12463012	0.90[ASN][1000 genomes]
rs12974130	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12974446	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1625762	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1643422	1.00[CHB][hapmap]
rs1673083	1.00[ASN][1000 genomes]
rs16960966	0.82[AMR][1000 genomes]
rs16971568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs16971769	0.94[AMR][1000 genomes]
rs16973489	1.00[ASN][1000 genomes]
rs16989369	0.82[AMR][1000 genomes]
rs17468285	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[ASN][1000 genomes]
rs17842485	0.82[AMR][1000 genomes]
rs1990964	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs25419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs28398875	1.00[AFR][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[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34106502	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35621405	1.00[ASN][1000 genomes]
rs35706444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3859520	1.00[AFR][1000 genomes];0.94[AMR][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[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]
rs8107274	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs8111419	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
6	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv911650	chr19:37241141-37331614	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv963042	chr19:37271305-37296858	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
16	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
20	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
21	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37287400-37327400	ZNF genes & repeats	Liver	Liver
2	chr19:37287800-37294800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:37289000-37295000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:37289000-37296400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:37289000-37309200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:37289200-37300600	Weak transcription	Right Ventricle	heart
7	chr19:37289200-37301600	Weak transcription	HSMMtube	muscle
8	chr19:37289200-37327000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:37289400-37295400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:37289400-37295600	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr19:37289400-37327600	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:37289600-37294800	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:37289600-37296800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:37289600-37301000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:37289600-37302200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:37289600-37302200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:37289600-37327400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:37289600-37327400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr19:37289800-37295000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr19:37289800-37295400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:37289800-37297600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:37290000-37301800	Weak transcription	Fetal Heart	heart
23	chr19:37290200-37295400	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:37290200-37295400	Strong transcription	Left Ventricle	heart
25	chr19:37290400-37294800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:37290800-37295600	ZNF genes & repeats	Fetal Stomach	stomach
27	chr19:37290800-37297200	Weak transcription	Stomach Mucosa	stomach
28	chr19:37291000-37298200	Weak transcription	NHDF-Ad	bronchial
29	chr19:37291200-37295400	Weak transcription	Dnd41	blood
30	chr19:37291600-37294800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr19:37291600-37298800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:37291800-37295600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:37292000-37294800	Strong transcription	Osteobl	bone
34	chr19:37292000-37296400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:37292000-37297000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:37292000-37303400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:37292000-37328400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:37292200-37299400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:37292200-37309400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:37292400-37294800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr19:37292400-37295000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr19:37292600-37295600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:37292600-37298200	Weak transcription	Brain Angular Gyrus	brain
44	chr19:37292800-37294800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:37292800-37297400	ZNF genes & repeats	Primary T cells from cord blood	blood
46	chr19:37293000-37295200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr19:37293000-37295200	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr19:37293200-37294800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr19:37293200-37295000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:37293200-37295000	ZNF genes & repeats	Thymus	Thymus

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