Variant report

Variant	rs12109288
Chromosome Location	chr5:98397073-98397074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98396979..98399832-chr5:98400023..98401845,2	K562	blood:
2	chr5:98239512..98242254-chr5:98395636..98397336,2	K562	blood:
3	chr5:98263463..98264993-chr5:98394604..98397406,2	K562	blood:
4	chr5:98262821..98265314-chr5:98397018..98399137,2	MCF-7	breast:
5	chr5:98386273..98389246-chr5:98395943..98397711,2	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12109206	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12109308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166576	0.89[YRI][hapmap]
rs17166582	0.82[YRI][hapmap]
rs6879498	0.93[EUR][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	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98393200-98397800	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:98395000-98398200	Enhancers	GM12878-XiMat	blood
3	chr5:98395800-98397200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:98396000-98397200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:98396000-98397400	Enhancers	Adipose Nuclei	Adipose
6	chr5:98396000-98397600	Flanking Active TSS	NH-A	brain
7	chr5:98396200-98397800	Enhancers	Primary B cells from cord blood	blood
8	chr5:98396400-98397400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:98396400-98397600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:98396400-98397600	Flanking Active TSS	NHDF-Ad	bronchial
11	chr5:98396400-98397600	Flanking Active TSS	NHLF	lung
12	chr5:98396400-98397800	Enhancers	HSMM	muscle
13	chr5:98396400-98398000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:98396400-98398000	Enhancers	HMEC	breast
15	chr5:98396400-98398200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:98396400-98398200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:98396600-98397200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:98396600-98397200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr5:98396600-98397400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:98396600-98397400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:98396600-98397400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr5:98396600-98397400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:98396600-98397400	Enhancers	Esophagus	oesophagus
24	chr5:98396600-98397400	Enhancers	HSMMtube	muscle
25	chr5:98396600-98397600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:98396600-98397600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:98396600-98397600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:98396600-98397600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:98396600-98397600	Enhancers	HepG2	liver
30	chr5:98396600-98397600	Flanking Active TSS	NHEK	skin
31	chr5:98396600-98397600	Flanking Active TSS	Osteobl	bone
32	chr5:98396600-98398000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:98396600-98398400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:98396800-98397200	Enhancers	Spleen	Spleen
35	chr5:98396800-98397400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:98396800-98399000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:98397000-98397200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:98397000-98397400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr5:98397000-98397600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:98397000-98398000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:98397000-98398000	Enhancers	Monocytes-CD14+_RO01746	blood

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