Variant report

Variant	rs12188882
Chromosome Location	chr5:60603643-60603644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60603025..60605964-chr5:60611139..60612666,2	MCF-7	breast:
2	chr5:60600516..60602032-chr5:60603241..60605744,2	MCF-7	breast:
3	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10044518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159373	1.00[JPT][hapmap]
rs28685817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs295523	1.00[JPT][hapmap]
rs295525	1.00[JPT][hapmap]
rs295526	1.00[JPT][hapmap]
rs295529	1.00[JPT][hapmap]
rs295530	1.00[JPT][hapmap]
rs295568	1.00[JPT][hapmap]
rs295580	1.00[JPT][hapmap]
rs298624	1.00[JPT][hapmap]
rs298626	1.00[JPT][hapmap]
rs298627	1.00[JPT][hapmap]
rs298628	1.00[JPT][hapmap]
rs298630	1.00[JPT][hapmap]
rs298631	1.00[JPT][hapmap]
rs4256302	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4323189	0.90[ASN][1000 genomes]
rs4382119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4452517	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs498497	1.00[JPT][hapmap]
rs557092	1.00[JPT][hapmap]
rs59628996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603018	1.00[JPT][hapmap]
rs73105361	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73105363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60597000-60605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:60598200-60606600	Weak transcription	Lung	lung
3	chr5:60600600-60605200	Enhancers	NHLF	lung
4	chr5:60600600-60609800	Weak transcription	Ovary	ovary
5	chr5:60600800-60615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:60601000-60606800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:60601200-60604600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:60601400-60603800	Enhancers	Hela-S3	cervix
9	chr5:60601400-60604400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:60601600-60603800	Enhancers	NHEK	skin
11	chr5:60602000-60603800	Enhancers	Fetal Intestine Small	intestine
12	chr5:60602000-60605000	Enhancers	NH-A	brain
13	chr5:60602200-60603800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:60602200-60603800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr5:60602200-60604400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:60602200-60605200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:60602400-60605200	Enhancers	HSMM	muscle
18	chr5:60602800-60604600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:60602800-60606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:60602800-60608200	Weak transcription	HMEC	breast
21	chr5:60603000-60607800	Weak transcription	HSMMtube	muscle
22	chr5:60603000-60608200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:60603200-60603800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:60603200-60603800	Enhancers	Osteobl	bone
25	chr5:60603200-60604400	Enhancers	A549	lung
26	chr5:60603200-60605000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:60603200-60605000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr5:60603200-60605400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:60603200-60605400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:60603200-60605400	Enhancers	NHDF-Ad	bronchial
31	chr5:60603200-60607200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:60603200-60609800	Weak transcription	Fetal Lung	lung
33	chr5:60603200-60609800	Weak transcription	Stomach Mucosa	stomach
34	chr5:60603400-60604600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:60603400-60605000	Weak transcription	Placenta	Placenta
36	chr5:60603600-60603800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr5:60603600-60607800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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