Variant report

Variant	rs28850384
Chromosome Location	chr15:41971152-41971153
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	chr15:41965662..41968571-chr15:41970591..41972884,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1107858	0.85[ASN][1000 genomes]
rs11634956	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637341	0.93[ASN][1000 genomes]
rs12440747	0.81[ASN][1000 genomes]
rs16952372	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971976	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677199	0.93[ASN][1000 genomes]
rs17677991	0.81[ASN][1000 genomes]
rs17678138	0.81[ASN][1000 genomes]
rs2004162	0.93[ASN][1000 genomes]
rs2412622	0.92[ASN][1000 genomes]
rs2577960	0.82[ASN][1000 genomes]
rs28556632	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700954	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28810086	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924570	0.93[ASN][1000 genomes]
rs62002066	0.93[ASN][1000 genomes]
rs62003900	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171123	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035855	0.84[EUR][1000 genomes];0.81[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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28850384	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
3	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
5	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
6	chr15:41954800-41976200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:41955000-41972600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:41958400-41978400	Weak transcription	Pancreas	Pancrea
11	chr15:41958800-41973400	Weak transcription	HMEC	breast
12	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
14	chr15:41959600-41981000	Weak transcription	Osteobl	bone
15	chr15:41961600-41975400	Weak transcription	Aorta	Aorta
16	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:41962000-41980200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:41962000-41983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
20	chr15:41962000-41990800	Weak transcription	NH-A	brain
21	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:41962000-42001400	Weak transcription	Gastric	stomach
23	chr15:41962200-41971800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:41962200-41972000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:41962200-41974800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:41962200-41984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:41962400-41971400	Weak transcription	Fetal Thymus	thymus
29	chr15:41962600-41973000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:41962600-41981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:41962600-41981800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:41962600-41983400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:41962600-41983600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:41962600-41984000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:41962800-41971200	Weak transcription	Fetal Intestine Large	intestine
37	chr15:41962800-41971400	Weak transcription	HSMM	muscle
38	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
39	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
40	chr15:41964400-41973600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:41964400-41975800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:41964600-41981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:41964600-41982200	Weak transcription	Ovary	ovary
44	chr15:41964800-41971800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:41964800-41972600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:41964800-41974800	Weak transcription	Primary T cells from cord blood	blood
47	chr15:41964800-41983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:41965000-41980600	Weak transcription	K562	blood
49	chr15:41965000-41982400	Weak transcription	Brain Anterior Caudate	brain
50	chr15:41965200-41971800	Weak transcription	Fetal Lung	lung

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