Variant report

Variant	rs555001
Chromosome Location	chr15:43545728-43545729
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	chr15:43545679..43548058-chr15:43549487..43551092,2	K562	blood:
2	chr15:43528880..43530995-chr15:43543131..43545896,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1095389	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853991	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1814323	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278857	0.91[MEX][hapmap]
rs2412781	0.87[MEX][hapmap]
rs2467745	0.83[MEX][hapmap]
rs2602141	0.83[MEX][hapmap]
rs35278581	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809482	0.87[MEX][hapmap]
rs4296223	0.87[MEX][hapmap]
rs4547312	0.92[MEX][hapmap]
rs471122	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473554	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475227	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491804	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs493177	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs493444	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498227	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501884	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505249	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512431	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513970	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs518234	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518261	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523737	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526292	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs530188	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530683	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs536313	0.83[MEX][hapmap]
rs538238	0.86[JPT][hapmap]
rs546722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs554001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556851	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs560134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572959	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573615	0.91[MEX][hapmap]
rs574065	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579651	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493083	0.87[MEX][hapmap]
rs690276	0.83[MEX][hapmap]
rs7163288	0.87[MEX][hapmap]
rs825733	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs825734	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9920879	0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs555001	TGM5	cis	lymphoblastoid	seeQTL
rs555001	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs555001	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs555001	ADAL	cis	lung	GTEx
rs555001	ADAL	cis	Adipose Subcutaneous	GTEx
rs555001	C15orf52	cis	cerebellum	SCAN
rs555001	TGM5	cis	Lymphoblastoid	GTEx
rs555001	TP53BP1	cis	parietal	SCAN
rs555001	ADAL	cis	parietal	SCAN
rs555001	WDR76	cis	parietal	SCAN
rs555001	ADAL	cis	Artery Tibial	GTEx
rs555001	TGM5	cis	multi-tissue	Pritchard
rs555001	ADAL	cis	Nerve Tibial	GTEx
rs555001	RTF1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43538000-43546600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr15:43542200-43546200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:43542600-43545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:43542800-43545800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:43544800-43546200	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:43545000-43546400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr15:43545000-43546600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:43545000-43546600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:43545200-43546600	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:43545200-43546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:43545200-43547000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:43545400-43546600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr15:43545400-43546600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:43545400-43546800	Enhancers	HMEC	breast
15	chr15:43545400-43546800	Enhancers	NHEK	skin
16	chr15:43545400-43547000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:43545600-43545800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:43545600-43545800	Enhancers	Spleen	Spleen
19	chr15:43545600-43546400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:43545600-43546400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:43545600-43546600	Enhancers	Esophagus	oesophagus
22	chr15:43545600-43546600	Bivalent Enhancer	NH-A	brain
23	chr15:43545600-43546800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:43545600-43546800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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