Variant report

Variant	rs17013030
Chromosome Location	chr12:86019935-86019936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:86014804..86017595-chr12:86018520..86021053,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11116993	0.83[AMR][1000 genomes]
rs11833551	1.00[AMR][1000 genomes]
rs12316200	0.83[AMR][1000 genomes]
rs12316964	0.83[AMR][1000 genomes]
rs12319540	0.83[AMR][1000 genomes]
rs12320271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013093	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013165	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013264	1.00[AMR][1000 genomes]
rs17013270	1.00[AMR][1000 genomes]
rs4316582	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59165763	1.00[AMR][1000 genomes]
rs61390175	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294826	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7298392	1.00[AMR][1000 genomes]
rs7301672	1.00[AMR][1000 genomes]
rs7309356	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7316003	0.83[AMR][1000 genomes]
rs73371080	1.00[AMR][1000 genomes]
rs73371084	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73373093	1.00[AMR][1000 genomes]
rs73373095	1.00[AMR][1000 genomes]
rs73373096	1.00[AMR][1000 genomes]
rs73374906	1.00[AMR][1000 genomes]
rs73374908	1.00[AMR][1000 genomes]
rs73374909	1.00[AMR][1000 genomes]
rs7953396	0.83[AMR][1000 genomes]
rs7966095	0.83[AMR][1000 genomes]
rs7972166	0.83[AMR][1000 genomes]
rs7973406	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751125	chr12:85884858-86098240	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1043253	chr12:85888151-86125364	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1037938	chr12:85902517-86045125	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2761758	chr12:85906092-86045137	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv455679	chr12:85908396-86024749	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv559664	chr12:85908396-86024749	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv559665	chr12:85908396-86070692	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2751126	chr12:85912432-86061403	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1054475	chr12:85985510-86175711	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv541561	chr12:85985510-86175711	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv430522	chr12:86010755-86069542	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1042467	chr12:86017619-86078149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86015200-86020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:86018400-86022000	Enhancers	Hela-S3	cervix
3	chr12:86019000-86022000	Enhancers	HUVEC	blood vessel
4	chr12:86019200-86021200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:86019400-86020000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:86019400-86021800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:86019600-86020800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:86019600-86021000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:86019600-86021400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:86019600-86021600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:86019600-86021800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:86019600-86021800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:86019600-86021800	Enhancers	HMEC	breast
14	chr12:86019600-86021800	Enhancers	HSMM	muscle
15	chr12:86019600-86021800	Enhancers	NH-A	brain
16	chr12:86019600-86021800	Enhancers	NHDF-Ad	bronchial
17	chr12:86019600-86021800	Enhancers	NHLF	lung
18	chr12:86019600-86022000	Enhancers	Osteobl	bone
19	chr12:86019800-86020000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:86019800-86020200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:86019800-86020400	Enhancers	NHEK	skin
22	chr12:86019800-86020800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:86019800-86021200	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:86019800-86021600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:86019800-86021800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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