Variant report

Variant	rs12608729
Chromosome Location	chr19:19700552-19700553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19700427-19700812	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:19700539-19701290	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19699647..19703848-chr19:19728208..19731865,4	MCF-7	breast:
2	chr19:19699149..19708161-chr19:19735507..19742255,11	MCF-7	breast:

Variant related genes	Relation type
PHF5CP	TF binding region
ENSG00000064547	Chromatin interaction
ENSG00000105717	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10500212	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12610185	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12610191	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996148	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16996185	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17216525	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17216588	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17217098	0.87[EUR][1000 genomes]
rs3794991	0.86[AMR][1000 genomes]
rs57504626	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58847337	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004926	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004933	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004951	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73004959	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73004962	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004966	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73004967	0.85[EUR][1000 genomes]
rs73004975	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19671600-19701800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19676200-19701600	Weak transcription	GM12878-XiMat	blood
4	chr19:19681200-19701600	Weak transcription	NHLF	lung
5	chr19:19681400-19701600	Weak transcription	Fetal Lung	lung
6	chr19:19681600-19701600	Weak transcription	Esophagus	oesophagus
7	chr19:19681600-19703200	Weak transcription	Dnd41	blood
8	chr19:19682000-19702200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:19682600-19700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:19686600-19700600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:19687000-19701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:19689800-19700600	Weak transcription	Thymus	Thymus
13	chr19:19689800-19701800	Weak transcription	Fetal Brain Female	brain
14	chr19:19691200-19700600	Weak transcription	Primary T cells from cord blood	blood
15	chr19:19693000-19701600	Weak transcription	Fetal Stomach	stomach
16	chr19:19693200-19701000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:19693200-19702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:19693400-19700600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:19696000-19700600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:19696400-19701600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:19696600-19702000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19698400-19702200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:19698800-19708400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:19699000-19703200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr19:19699200-19700800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr19:19699200-19701000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:19699200-19701600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:19699200-19701600	Weak transcription	Fetal Brain Male	brain
29	chr19:19699400-19702400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr19:19699400-19702800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:19699400-19703000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:19699600-19700600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:19699600-19700600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:19699800-19700600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:19699800-19701000	Weak transcription	Brain Germinal Matrix	brain
36	chr19:19699800-19701000	Weak transcription	HMEC	breast
37	chr19:19699800-19701600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19700200-19702600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr19:19700400-19700800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:19700400-19701600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:19700400-19701800	Enhancers	NHDF-Ad	bronchial
42	chr19:19700400-19702600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:19700400-19703000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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