Variant report

Variant	rs2039028
Chromosome Location	chr10:21638971-21638972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:21629419..21631045-chr10:21637686..21640023,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10828236	0.86[ASN][1000 genomes]
rs11012667	0.82[ASN][1000 genomes]
rs12244309	0.82[JPT][hapmap]
rs12269541	0.83[EUR][1000 genomes]
rs16921729	1.00[CHB][hapmap]
rs2039027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324716	0.85[ASN][1000 genomes]
rs6482176	0.82[ASN][1000 genomes]
rs7068408	0.85[CHD][hapmap];0.87[GIH][hapmap]
rs7091815	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7092545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7098605	0.91[AMR][1000 genomes]
rs71491180	0.82[ASN][1000 genomes]
rs7895221	0.82[ASN][1000 genomes]
rs7898040	0.85[CHD][hapmap];0.87[GIH][hapmap]
rs7898836	0.86[ASN][1000 genomes]
rs7905484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7909938	0.80[ASN][1000 genomes]
rs7913493	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7914447	0.82[ASN][1000 genomes]
rs7920204	0.82[ASN][1000 genomes]
rs7923649	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7923849	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530148	chr10:21065080-21724565	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv831807	chr10:21509185-21688043	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2039028	NEBL-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:21626400-21639200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:21627000-21639000	Weak transcription	NHEK	skin
3	chr10:21637400-21639600	Enhancers	Fetal Muscle Leg	muscle
4	chr10:21638000-21639200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:21638000-21639600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:21638000-21639600	Enhancers	Fetal Lung	lung
7	chr10:21638200-21639600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:21638400-21639600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:21638600-21639600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:21638600-21639600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:21638600-21639600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:21638600-21639600	Flanking Active TSS	A549	lung
13	chr10:21638600-21639600	Enhancers	NHLF	lung
14	chr10:21638600-21640000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr10:21638600-21640200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:21638800-21639200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:21638800-21639200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr10:21638800-21639200	Enhancers	HSMMtube	muscle
19	chr10:21638800-21639400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr10:21638800-21639400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:21638800-21639400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr10:21638800-21639400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:21638800-21639400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:21638800-21639400	Flanking Active TSS	Fetal Heart	heart
25	chr10:21638800-21639600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr10:21638800-21639600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:21638800-21639600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:21638800-21639600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr10:21638800-21639600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr10:21638800-21639600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr10:21638800-21639600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:21638800-21639600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr10:21638800-21639600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:21638800-21639600	Enhancers	Aorta	Aorta
35	chr10:21638800-21639600	Enhancers	Colon Smooth Muscle	Colon
36	chr10:21638800-21639600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr10:21638800-21639600	Enhancers	Gastric	stomach
38	chr10:21638800-21639600	Enhancers	Left Ventricle	heart
39	chr10:21638800-21639600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr10:21638800-21639600	Enhancers	Rectal Smooth Muscle	rectum
41	chr10:21638800-21639600	Enhancers	Right Atrium	heart
42	chr10:21638800-21639600	Bivalent Enhancer	HepG2	liver
43	chr10:21638800-21639600	Enhancers	HMEC	breast
44	chr10:21638800-21639600	Enhancers	NH-A	brain
45	chr10:21638800-21639600	Enhancers	Osteobl	bone
46	chr10:21638800-21639800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:21638800-21639800	Enhancers	Fetal Intestine Large	intestine
48	chr10:21638800-21639800	Enhancers	Ovary	ovary
49	chr10:21638800-21639800	Enhancers	Stomach Smooth Muscle	stomach
50	chr10:21638800-21640000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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