Variant report

Variant	rs10438299
Chromosome Location	chr15:41871908-41871909
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41861308..41862926-chr15:41869698..41872291,2	K562	blood:
2	chr15:41870467..41873632-chr15:41874350..41878118,3	K562	blood:
3	chr15:41870694..41874947-chr15:41876174..41878118,3	K562	blood:

Variant related genes	Relation type
ENSG00000092445	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1077714	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906912	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12915829	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246444	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2277537	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2289743	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2482307	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28655000	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28792443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28844285	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784283	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924552	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924559	0.87[ASN][1000 genomes]
rs6493004	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6493005	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs66906913	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68058196	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166371	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183231	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025165	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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	esv3312194	chr15:41868660-41873158	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3312195	chr15:41868660-41873158	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10438299	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:41852600-41877400	Weak transcription	HMEC	breast
4	chr15:41852800-41877400	Weak transcription	NHEK	skin
5	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
6	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
7	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:41861000-41877200	Weak transcription	HUVEC	blood vessel
10	chr15:41861200-41877000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:41861400-41873200	Weak transcription	K562	blood
12	chr15:41863800-41873000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:41864200-41877000	Weak transcription	Fetal Kidney	kidney
14	chr15:41865800-41877000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:41865800-41877000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:41865800-41877200	Weak transcription	NHLF	lung
17	chr15:41867600-41877200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:41867600-41877200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:41868000-41877000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:41868000-41877400	Weak transcription	Esophagus	oesophagus
21	chr15:41871000-41872000	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:41871000-41877200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:41871200-41872600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41871200-41873000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:41871200-41876800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:41871200-41877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:41871200-41877000	Weak transcription	Fetal Brain Female	brain
28	chr15:41871200-41877000	Weak transcription	Spleen	Spleen
29	chr15:41871200-41877200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:41871200-41877200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:41871200-41877200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:41871200-41877200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:41871200-41877200	Weak transcription	Right Atrium	heart
34	chr15:41871200-41877400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:41871200-41877400	Weak transcription	Gastric	stomach
36	chr15:41871400-41873000	Weak transcription	Placenta	Placenta
37	chr15:41871400-41873000	Weak transcription	Dnd41	blood
38	chr15:41871400-41873400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:41871400-41873800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41871400-41874200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:41871400-41875600	Weak transcription	Fetal Intestine Large	intestine
42	chr15:41871400-41875800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:41871400-41876800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:41871400-41876800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:41871400-41877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:41871400-41877000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:41871400-41877000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:41871400-41877000	Weak transcription	Adipose Nuclei	Adipose
49	chr15:41871400-41877000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:41871400-41877200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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