Variant report

Variant	rs9863154
Chromosome Location	chr3:121721666-121721667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10934568	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10934570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637573	0.83[EUR][1000 genomes]
rs13074085	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1920289	0.86[EUR][1000 genomes]
rs2332034	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4325959	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793566	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6793858	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9811389	0.86[EUR][1000 genomes]
rs9812869	0.86[EUR][1000 genomes]
rs9824120	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825193	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844039	0.86[EUR][1000 genomes]
rs9871743	0.86[EUR][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	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9863154	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:121709600-121721800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
4	chr3:121715400-121723400	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:121715400-121723400	Weak transcription	Fetal Thymus	thymus
6	chr3:121717600-121721800	Weak transcription	HMEC	breast
7	chr3:121717800-121722200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:121718600-121721800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:121718800-121722000	Weak transcription	NHEK	skin
10	chr3:121719400-121722000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:121720000-121723400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:121720200-121722000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:121720200-121723200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:121720200-121723200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:121720200-121723400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:121720200-121723400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:121720200-121723400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:121720200-121723600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:121720400-121721800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:121720400-121722200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:121720400-121723400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:121720400-121723400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:121720400-121725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:121720600-121723200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:121720600-121724400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:121720800-121732200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:121720800-121732200	Weak transcription	Pancreas	Pancrea
28	chr3:121721000-121723400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:121721200-121722800	Enhancers	Fetal Kidney	kidney
30	chr3:121721200-121724000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr3:121721400-121721800	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:121721400-121721800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:121721400-121722000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:121721400-121722000	Active TSS	Rectal Smooth Muscle	rectum
35	chr3:121721400-121722400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr3:121721400-121723600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:121721600-121721800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:121721600-121722000	Enhancers	Colonic Mucosa	Colon
39	chr3:121721600-121722000	Enhancers	Lung	lung
40	chr3:121721600-121722200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:121721600-121722200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:121721600-121722400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr3:121721600-121722600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr3:121721600-121722600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:121721600-121723400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:121721600-121723800	Enhancers	NH-A	brain
47	chr3:121721600-121724000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:121721600-121724000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:121721600-121724600	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:121721600-121725200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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