Variant report

Variant	rs12974028
Chromosome Location	chr19:19666506-19666507
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	chr19:19665908..19668472-chr19:19672095..19673816,2	MCF-7	breast:
2	chr19:19662679..19666919-chr19:19737231..19739849,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12611058	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977917	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981270	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12982628	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985142	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1476459	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33982830	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34096655	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34316070	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34316527	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34324119	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34424437	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35209041	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35437712	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35553578	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35842591	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56083851	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62134460	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62137783	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62137816	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137820	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137822	0.85[EUR][1000 genomes]
rs7247165	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73004920	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750216	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19652000-19688400	Weak transcription	Right Atrium	heart
3	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:19652600-19686200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:19659200-19686200	Weak transcription	Fetal Brain Male	brain
6	chr19:19661200-19670800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:19661400-19675600	Weak transcription	Ovary	ovary
8	chr19:19661400-19677800	Weak transcription	Fetal Lung	lung
9	chr19:19661600-19673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:19661800-19673400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:19662400-19669600	Weak transcription	Thymus	Thymus
12	chr19:19663400-19669200	Weak transcription	Fetal Brain Female	brain
13	chr19:19663400-19670800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:19663600-19669600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:19665000-19669000	Weak transcription	GM12878-XiMat	blood
16	chr19:19665600-19668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:19665600-19669600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:19665600-19669600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:19665600-19670400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:19665600-19672600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19665600-19677200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:19665600-19682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:19665600-19685600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:19665800-19669400	Weak transcription	Fetal Stomach	stomach
25	chr19:19665800-19670400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr19:19665800-19670400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:19665800-19670800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:19665800-19672600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:19666400-19666600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:19666400-19672800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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