Variant report

Variant	rs28407836
Chromosome Location	chr15:43182539-43182540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11070385	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11631404	0.84[EUR][1000 genomes]
rs1197533	1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes]
rs12050604	0.83[EUR][1000 genomes]
rs1206698	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12437637	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12904179	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913213	0.85[EUR][1000 genomes]
rs12913586	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13329073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381855	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2056346	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2126603	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2169581	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2277532	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682074	0.98[EUR][1000 genomes]
rs28646262	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715020	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28805017	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28890597	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923952	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4923956	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4924702	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56114844	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58745709	0.83[EUR][1000 genomes]
rs62020697	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62020699	0.81[AMR][1000 genomes]
rs62020706	0.85[EUR][1000 genomes]
rs6493067	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs6493068	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6493069	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167802	0.96[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7168141	0.82[EUR][1000 genomes]
rs7169603	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7173097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173782	0.82[EUR][1000 genomes]
rs7176915	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7178752	0.81[AMR][1000 genomes]
rs7182753	1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs7496079	0.83[EUR][1000 genomes]
rs8025479	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8028731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8028822	0.85[AMR][1000 genomes]
rs8035752	0.96[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs8036096	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8037374	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs9806175	1.00[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3490431	chr15:43148709-43190630	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3490432	chr15:43148709-43190630	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv3408090	chr15:43172709-43207571	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3366604	chr15:43172709-43210677	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3408604	chr15:43175709-43207571	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28407836	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43132000-43186800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr15:43155000-43182600	Weak transcription	Primary T cells from cord blood	blood
3	chr15:43177800-43185400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:43178600-43182600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:43180200-43185600	Enhancers	Placenta	Placenta
6	chr15:43180800-43182800	Weak transcription	Right Ventricle	heart
7	chr15:43181000-43182600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:43181000-43182800	Weak transcription	Psoas Muscle	Psoas
9	chr15:43181000-43184000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:43181800-43184400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:43181800-43184400	Enhancers	HUVEC	blood vessel
12	chr15:43182000-43182600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr15:43182000-43184000	Enhancers	HMEC	breast
14	chr15:43182200-43182600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr15:43182200-43183200	Enhancers	HSMMtube	muscle
16	chr15:43182200-43184000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:43182200-43184400	Enhancers	NHDF-Ad	bronchial
18	chr15:43182400-43182600	Enhancers	Lung	lung
19	chr15:43182400-43182800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:43182400-43182800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:43182400-43182800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:43182400-43182800	Enhancers	Brain Anterior Caudate	brain
23	chr15:43182400-43182800	Flanking Active TSS	NH-A	brain
24	chr15:43182400-43182800	Flanking Active TSS	NHEK	skin
25	chr15:43182400-43183000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr15:43182400-43183200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:43182400-43183200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:43182400-43183200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:43182400-43183200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr15:43182400-43183200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr15:43182400-43183200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr15:43182400-43183200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:43182400-43183200	Enhancers	Fetal Heart	heart
34	chr15:43182400-43183200	Enhancers	Left Ventricle	heart
35	chr15:43182400-43183200	Enhancers	Right Atrium	heart
36	chr15:43182400-43183200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:43182400-43183600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:43182400-43183600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:43182400-43184200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr15:43182400-43184200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:43182400-43184200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:43182400-43184200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:43182400-43184200	Enhancers	Aorta	Aorta
44	chr15:43182400-43184200	Enhancers	HSMM	muscle
45	chr15:43182400-43184200	Enhancers	Osteobl	bone
46	chr15:43182400-43184400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:43182400-43184400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:43182400-43184800	Enhancers	Pancreas	Pancrea

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