Variant report

Variant	rs9824120
Chromosome Location	chr3:121717577-121717578
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	chr3:121716594..121718488-chr3:121741202..121742786,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10934568	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10934570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637573	0.83[EUR][1000 genomes]
rs13074085	0.86[EUR][1000 genomes]
rs1920289	0.86[EUR][1000 genomes]
rs2001212	0.93[CHB][hapmap]
rs2332034	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332036	0.84[MEX][hapmap]
rs2700421	0.80[CHB][hapmap]
rs3805138	0.81[CHB][hapmap]
rs4325959	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793566	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6793858	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9811389	0.86[EUR][1000 genomes]
rs9812869	0.86[EUR][1000 genomes]
rs9816720	0.81[CHB][hapmap];0.89[MEX][hapmap]
rs9825193	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844039	0.86[EUR][1000 genomes]
rs9863154	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9824120	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9824120	MUC13	cis	cerebellum	SCAN
rs9824120	SLC15A2	cis	parietal	SCAN
rs9824120	SLC15A2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:121706000-121721200	Weak transcription	Fetal Kidney	kidney
4	chr3:121708800-121718000	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:121709200-121719200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:121709600-121721800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:121712200-121718800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:121712800-121721600	Weak transcription	Colonic Mucosa	Colon
9	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
10	chr3:121713200-121717800	Enhancers	Adipose Nuclei	Adipose
11	chr3:121713200-121719000	Enhancers	HUVEC	blood vessel
12	chr3:121713400-121718600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:121713400-121718800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:121713800-121718400	Enhancers	Primary B cells from cord blood	blood
15	chr3:121714000-121718000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:121714200-121717800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:121714400-121719800	Weak transcription	Lung	lung
18	chr3:121714600-121719200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:121714800-121719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:121714800-121719600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:121714800-121720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:121715000-121719400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:121715000-121719600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:121715200-121717600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:121715400-121723400	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:121715400-121723400	Weak transcription	Fetal Thymus	thymus
27	chr3:121716000-121717800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:121716000-121718000	Enhancers	Fetal Intestine Large	intestine
29	chr3:121716200-121717600	Enhancers	HMEC	breast
30	chr3:121716200-121717800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:121716200-121718000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:121716200-121718000	Enhancers	Fetal Intestine Small	intestine
33	chr3:121716200-121718000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr3:121716200-121718600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:121716200-121718800	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:121716200-121720800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:121716400-121717600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:121716400-121717800	Enhancers	Spleen	Spleen
39	chr3:121716400-121718000	Enhancers	NH-A	brain
40	chr3:121716600-121717600	Enhancers	Osteobl	bone
41	chr3:121716600-121717800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:121716600-121719800	Weak transcription	Pancreas	Pancrea
43	chr3:121716600-121720000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:121716800-121717600	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr3:121716800-121717800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:121717000-121717800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr3:121717200-121717800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:121717200-121718000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:121717200-121718000	Enhancers	Hela-S3	cervix
50	chr3:121717200-121721600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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