Variant report

Variant	rs28754734
Chromosome Location	chr15:42093152-42093153
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	chr15:42084827..42086940-chr15:42091346..42094330,2	K562	blood:
2	chr15:42090667..42093233-chr15:42097205..42099737,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1105881	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11632424	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635067	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11635415	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637341	0.81[EUR][1000 genomes]
rs12440747	0.89[EUR][1000 genomes]
rs12441300	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531140	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17677199	0.81[EUR][1000 genomes]
rs17677991	0.89[EUR][1000 genomes]
rs17678138	0.89[EUR][1000 genomes]
rs17678552	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17678767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17734856	0.86[EUR][1000 genomes]
rs1918310	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2004162	0.81[EUR][1000 genomes]
rs2241522	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2277535	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303516	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303518	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305654	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2412622	0.81[EUR][1000 genomes]
rs2412641	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577960	0.89[EUR][1000 genomes]
rs28373318	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28401754	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28432037	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28451764	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28680296	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28701757	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3179542	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3743024	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3959569	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923910	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923914	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923915	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924575	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924576	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924580	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62002090	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62002091	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025714	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs890498	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs890505	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9920903	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases
7	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28754734	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
2	chr15:42083600-42104600	Weak transcription	Liver	Liver
3	chr15:42083600-42109200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42083800-42096600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42083800-42098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:42083800-42098600	Weak transcription	Pancreas	Pancrea
7	chr15:42083800-42098600	Weak transcription	A549	lung
8	chr15:42083800-42103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:42083800-42103400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:42083800-42104400	Weak transcription	Colonic Mucosa	Colon
11	chr15:42083800-42105000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:42083800-42119400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:42084000-42098400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:42085200-42097400	Weak transcription	Psoas Muscle	Psoas
15	chr15:42085400-42093200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:42088600-42103000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:42089000-42096400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:42089400-42114800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:42089600-42096600	Weak transcription	Brain Angular Gyrus	brain
20	chr15:42089800-42094200	Strong transcription	Primary T cells from cord blood	blood
21	chr15:42089800-42096400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:42089800-42096400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:42089800-42096800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:42090000-42093600	Genic enhancers	NHEK	skin
25	chr15:42090000-42094200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:42090000-42096600	Weak transcription	Aorta	Aorta
27	chr15:42090000-42096600	Weak transcription	Brain Substantia Nigra	brain
28	chr15:42090000-42096600	Weak transcription	Fetal Kidney	kidney
29	chr15:42090000-42096600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:42090000-42097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:42090000-42109800	Weak transcription	Small Intestine	intestine
32	chr15:42090600-42101600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:42090800-42093600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:42091000-42093200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:42091000-42093600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:42091000-42094200	Strong transcription	Lung	lung
37	chr15:42091000-42094400	Strong transcription	Brain Anterior Caudate	brain
38	chr15:42091000-42096400	Strong transcription	Fetal Stomach	stomach
39	chr15:42091000-42096800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:42091200-42093400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr15:42091200-42093600	Genic enhancers	HMEC	breast
42	chr15:42091200-42094200	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:42091400-42093600	Strong transcription	Dnd41	blood
44	chr15:42091400-42096800	Weak transcription	Right Atrium	heart
45	chr15:42091400-42105400	Weak transcription	HSMMtube	muscle
46	chr15:42091600-42093400	Strong transcription	Thymus	Thymus
47	chr15:42091600-42093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:42091600-42093600	Strong transcription	Adipose Nuclei	Adipose
49	chr15:42091600-42094000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:42091600-42094200	Strong transcription	Primary B cells from cord blood	blood

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