Variant report

Variant	rs13077048
Chromosome Location	chr3:141106954-141106955
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141106008..141109150-chr3:141119369..141122507,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-3	chr3:141105714-141108679	NONHSAT092429

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13068733	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1344672	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1344674	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1582874	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991431	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2114867	0.86[ASN][1000 genomes]
rs2871960	0.90[EUR][1000 genomes]
rs4683605	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683606	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6440003	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6440006	0.82[EUR][1000 genomes]
rs6763927	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6763931	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6764769	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6785012	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808936	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724016	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7625643	0.81[EUR][1000 genomes]
rs7632381	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9846396	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853018	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
2	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
3	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
4	chr3:141091000-141107200	Weak transcription	Liver	Liver
5	chr3:141094800-141112200	Weak transcription	Spleen	Spleen
6	chr3:141096000-141111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:141098400-141107600	Weak transcription	Aorta	Aorta
8	chr3:141098600-141115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:141099000-141110400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:141099600-141109800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:141100600-141112400	Weak transcription	Lung	lung
12	chr3:141102400-141107600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:141102800-141111800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:141102800-141112000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:141103200-141107000	Genic enhancers	Osteobl	bone
16	chr3:141103200-141107600	Weak transcription	Hela-S3	cervix
17	chr3:141103200-141107800	Weak transcription	Stomach Mucosa	stomach
18	chr3:141103200-141111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:141103600-141107800	Strong transcription	HSMM	muscle
20	chr3:141103600-141110200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:141103800-141107600	Active TSS	Brain Angular Gyrus	brain
22	chr3:141103800-141109000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:141104000-141108800	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:141104000-141109600	Active TSS	Brain Anterior Caudate	brain
25	chr3:141104200-141107000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:141104200-141108200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:141104400-141108200	Active TSS	Primary T cells fromperipheralblood	blood
28	chr3:141104800-141107400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:141104800-141107600	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:141104800-141108400	Active TSS	Stomach Smooth Muscle	stomach
31	chr3:141105000-141108000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:141105200-141110200	Weak transcription	Fetal Heart	heart
33	chr3:141105400-141107000	Flanking Active TSS	NHEK	skin
34	chr3:141105600-141107000	Flanking Active TSS	Fetal Lung	lung
35	chr3:141105800-141107200	Strong transcription	A549	lung
36	chr3:141105800-141108000	Active TSS	Brain Germinal Matrix	brain
37	chr3:141105800-141110200	Weak transcription	Right Atrium	heart
38	chr3:141105800-141111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:141106000-141107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:141106000-141107600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:141106000-141107600	Weak transcription	Esophagus	oesophagus
42	chr3:141106000-141107600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:141106000-141107600	Weak transcription	HSMMtube	muscle
44	chr3:141106000-141107800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:141106000-141108800	Active TSS	Duodenum Mucosa	Duodenum
46	chr3:141106000-141109200	Active TSS	Fetal Brain Female	brain
47	chr3:141106000-141109800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:141106000-141110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:141106000-141110200	Weak transcription	Fetal Kidney	kidney
50	chr3:141106000-141111000	Weak transcription	Gastric	stomach

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