Variant report

Variant	rs4548810
Chromosome Location	chr15:52943814-52943815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1080731	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs10851521	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070907	0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070908	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070909	0.95[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11853917	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855616	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs11857150	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11858743	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12594964	0.80[ASN][1000 genomes]
rs12898644	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12902679	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs12914047	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914502	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12915981	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13329393	0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs17614559	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs1863512	0.95[CEU][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2288271	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs2414160	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2414161	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2414163	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414166	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2414167	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs28368342	0.80[ASN][1000 genomes]
rs34431049	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3751614	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4390542	0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4774634	0.91[CEU][hapmap]
rs4774636	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4776058	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs4776063	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4776065	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4776066	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776068	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7167494	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs8026800	0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8030141	0.88[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs933860	0.95[CEU][hapmap];0.89[CHB][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4548810	KIAA1370	cis	normal skin	skin_eQTL
rs4548810	MYO5A	cis	cerebellum	SCAN
rs4548810	KIAA1370	cis	uninvolved skin	skin_eQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
2	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
5	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
10	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
12	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:52908600-52956200	Weak transcription	Gastric	stomach
14	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
16	chr15:52915600-52944200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:52923200-52945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:52928000-52944000	Weak transcription	Fetal Intestine Small	intestine
21	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
22	chr15:52928000-52956400	Weak transcription	Lung	lung
23	chr15:52928200-52945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:52929400-52945200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:52929800-52944000	Weak transcription	Aorta	Aorta
26	chr15:52929800-52945200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:52931000-52944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:52935400-52944000	Weak transcription	Left Ventricle	heart
29	chr15:52935800-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:52938000-52945600	Weak transcription	Placenta	Placenta
31	chr15:52938800-52944000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:52938800-52945200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:52938800-52945800	Weak transcription	Psoas Muscle	Psoas
34	chr15:52939000-52944000	Weak transcription	Ovary	ovary
35	chr15:52939600-52945400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:52940000-52944200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:52940000-52945200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:52940200-52944000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:52940200-52944200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:52940200-52945400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:52942200-52944200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:52942800-52944000	Enhancers	HSMMtube	muscle
43	chr15:52942800-52944200	Active TSS	Fetal Brain Female	brain
44	chr15:52942800-52944600	Flanking Active TSS	Fetal Brain Male	brain
45	chr15:52943000-52944000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:52943200-52944400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:52943200-52944600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:52943400-52944000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr15:52943400-52944000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52943400-52944000	Enhancers	Skeletal Muscle Male	skeletal muscle

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