Variant report

Variant	rs12901238
Chromosome Location	chr15:92512624-92512625
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	chr15:92509487..92513090-chr15:92516971..92519490,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10454699	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852165	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852166	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635055	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12439826	0.93[ASN][1000 genomes]
rs12902685	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12905744	0.95[ASN][1000 genomes]
rs12909480	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12910715	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910862	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916491	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356417	0.99[ASN][1000 genomes]
rs1400783	0.95[ASN][1000 genomes]
rs1568210	0.93[ASN][1000 genomes]
rs16946157	0.85[ASN][1000 genomes]
rs16946164	0.85[ASN][1000 genomes]
rs16946168	0.85[ASN][1000 genomes]
rs2138849	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176452	0.97[ASN][1000 genomes]
rs28470895	0.85[ASN][1000 genomes]
rs28513490	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28752332	0.88[EUR][1000 genomes]
rs35973922	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4312282	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4932592	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4932593	0.94[ASN][1000 genomes]
rs62009549	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7165760	0.86[ASN][1000 genomes]
rs7171131	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171921	0.95[ASN][1000 genomes]
rs7172099	0.95[ASN][1000 genomes]
rs7178673	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7178734	0.98[ASN][1000 genomes]
rs7179815	0.85[ASN][1000 genomes]
rs8025507	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8027160	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8040046	0.96[ASN][1000 genomes]
rs953888	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs976216	0.99[ASN][1000 genomes]
rs9920069	0.82[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	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92506000-92513600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:92506000-92517600	Weak transcription	Colonic Mucosa	Colon
4	chr15:92507600-92514400	Enhancers	Fetal Heart	heart
5	chr15:92507600-92516400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:92507800-92513200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr15:92508000-92514000	Enhancers	Brain Angular Gyrus	brain
8	chr15:92508000-92515000	Enhancers	Brain Cingulate Gyrus	brain
9	chr15:92508600-92514200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:92508600-92517600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:92508800-92514400	Enhancers	Ovary	ovary
12	chr15:92508800-92517600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr15:92509000-92518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:92509200-92513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:92509600-92512800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:92509600-92512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:92509600-92512800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:92509600-92513000	Weak transcription	NHLF	lung
19	chr15:92509600-92515400	Enhancers	Brain Substantia Nigra	brain
20	chr15:92509600-92519200	Enhancers	Brain Hippocampus Middle	brain
21	chr15:92509800-92512800	Weak transcription	Adipose Nuclei	Adipose
22	chr15:92509800-92513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:92509800-92513000	Weak transcription	HSMM	muscle
24	chr15:92509800-92515200	Enhancers	Brain Anterior Caudate	brain
25	chr15:92510000-92513200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:92510000-92514200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:92510200-92512800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:92510200-92512800	Weak transcription	NHDF-Ad	bronchial
29	chr15:92510200-92513000	Weak transcription	HSMMtube	muscle
30	chr15:92510200-92513600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:92510800-92514400	Enhancers	Left Ventricle	heart
32	chr15:92511000-92514000	Enhancers	Right Atrium	heart
33	chr15:92511200-92514000	Enhancers	Aorta	Aorta
34	chr15:92511200-92514200	Enhancers	Lung	lung
35	chr15:92511600-92514200	Enhancers	Right Ventricle	heart
36	chr15:92511800-92513000	Weak transcription	Hela-S3	cervix
37	chr15:92511800-92513000	Weak transcription	Osteobl	bone
38	chr15:92511800-92513200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:92511800-92513800	Enhancers	Fetal Lung	lung
40	chr15:92511800-92514000	Enhancers	Fetal Brain Male	brain
41	chr15:92511800-92514200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr15:92512000-92513000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:92512000-92513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:92512000-92513000	Weak transcription	HMEC	breast
45	chr15:92512000-92513200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:92512000-92513200	Weak transcription	NHEK	skin
47	chr15:92512000-92516600	Weak transcription	A549	lung
48	chr15:92512200-92513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:92512200-92513000	Weak transcription	Esophagus	oesophagus
50	chr15:92512200-92513200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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