Variant report

Variant	rs12304259
Chromosome Location	chr12:49630288-49630289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49624204..49632381-chr12:49656851..49664182,36	K562	blood:
2	chr12:49495156..49497539-chr12:49627737..49630589,2	MCF-7	breast:
3	chr12:49480667..49484099-chr12:49627128..49630502,6	K562	blood:
4	chr12:49453100..49454681-chr12:49629053..49631692,2	MCF-7	breast:
5	chr12:49628615..49630966-chr12:49665293..49667047,2	K562	blood:
6	chr12:49523058..49526558-chr12:49627579..49630702,9	MCF-7	breast:
7	chr12:49624371..49632888-chr12:49655742..49664182,29	K562	blood:
8	chr12:49628644..49630691-chr12:49633942..49636514,2	MCF-7	breast:
9	chr12:49518847..49527600-chr12:49624546..49632235,69	K562	blood:
10	chr12:49626201..49630727-chr12:49631926..49634972,10	K562	blood:
11	chr12:49628427..49630609-chr12:49637819..49639701,2	MCF-7	breast:
12	chr12:49611550..49615135-chr12:49626761..49630349,3	MCF-7	breast:
13	chr12:49523889..49527940-chr12:49626125..49630578,10	MCF-7	breast:
14	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258101	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10047512	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10047588	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1109811	1.00[AMR][1000 genomes]
rs11168925	1.00[AMR][1000 genomes]
rs11168927	1.00[AMR][1000 genomes]
rs11168928	1.00[ASW][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168931	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168938	1.00[ASW][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11168939	1.00[AMR][1000 genomes]
rs11168940	1.00[AMR][1000 genomes]
rs11168942	1.00[AMR][1000 genomes]
rs11168955	0.87[YRI][hapmap]
rs12296231	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12296536	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297433	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12300386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300998	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12303188	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12304483	1.00[AMR][1000 genomes]
rs12304746	1.00[AMR][1000 genomes]
rs12308782	0.82[AFR][1000 genomes]
rs12309028	1.00[ASW][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12314967	0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318666	0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12322876	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28758893	1.00[AMR][1000 genomes]
rs9804936	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv518041	chr12:49618043-49645240	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49628800-49630400	Enhancers	NHDF-Ad	bronchial
2	chr12:49629000-49630800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:49629000-49632600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:49629200-49630400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:49629200-49630600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:49629200-49632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:49629200-49632600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:49629200-49633600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:49629200-49633800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:49629200-49634000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:49629200-49635000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:49629200-49653400	Weak transcription	Fetal Kidney	kidney
13	chr12:49629400-49630600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:49629400-49632600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:49629400-49634200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:49629400-49634200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:49629400-49637200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:49629400-49651000	Weak transcription	Fetal Brain Female	brain
19	chr12:49629400-49657800	Weak transcription	Fetal Stomach	stomach
20	chr12:49629800-49632200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:49630000-49630800	Enhancers	K562	blood

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