Variant report

Variant	rs1814323
Chromosome Location	chr15:43563237-43563238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:43562778-43563543	HL-60	blood:	n/a	chr15:43563141-43563154 chr15:43563140-43563153
2	POLR2A	chr15:43562717-43563576	HL-60	blood:	n/a	n/a
3	MAX	chr15:43562810-43563342	NB4	blood:	n/a	n/a
4	POLR2A	chr15:43562696-43563485	HL-60	blood:	n/a	n/a
5	MYC	chr15:43562844-43563322	NB4	blood:	n/a	n/a

Variant related genes	Relation type
TGM5	TF binding region
ATP5HP1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1095389	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070389	1.00[ASW][hapmap]
rs1133395	0.81[AMR][1000 genomes]
rs11853991	0.91[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs12102205	0.83[AMR][1000 genomes]
rs12148735	0.86[AMR][1000 genomes]
rs2244981	0.87[MEX][hapmap]
rs2278856	0.84[AMR][1000 genomes]
rs2278857	0.96[MEX][hapmap];0.82[AMR][1000 genomes]
rs2412781	0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs2467745	0.87[MEX][hapmap]
rs2602141	0.87[MEX][hapmap]
rs35278581	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809482	0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs4296223	0.91[MEX][hapmap]
rs4547312	0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs471122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473554	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475227	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475261	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478028	0.84[AMR][1000 genomes]
rs485148	0.84[AMR][1000 genomes]
rs489964	1.00[ASW][hapmap]
rs491800	0.83[AMR][1000 genomes]
rs491804	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492743	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498227	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501884	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502157	1.00[ASW][hapmap]
rs504417	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505249	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507178	0.85[AMR][1000 genomes]
rs510108	0.86[AMR][1000 genomes]
rs512431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512628	0.85[AMR][1000 genomes]
rs513970	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518234	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518261	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523737	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs526292	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530118	1.00[ASW][hapmap]
rs530188	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530683	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531910	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536313	0.87[MEX][hapmap]
rs538238	0.86[JPT][hapmap];0.84[MKK][hapmap]
rs546722	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552701	0.83[AMR][1000 genomes]
rs554001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555001	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]
rs556851	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs560134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564946	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565658	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572959	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573169	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573615	0.96[MEX][hapmap];0.84[AMR][1000 genomes]
rs574065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576557	0.86[AMR][1000 genomes]
rs579651	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493083	0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs690276	0.87[MEX][hapmap]
rs690367	0.87[MEX][hapmap]
rs694725	0.87[MEX][hapmap]
rs7163288	0.91[MEX][hapmap]
rs7166812	0.81[AMR][1000 genomes]
rs825733	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs825734	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920879	0.91[MEX][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3375708	chr15:43563184-43563528	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1814323	RTF1	cis	cerebellum	SCAN
rs1814323	ADAL	cis	Artery Tibial	GTEx
rs1814323	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs1814323	AC011330.5	cis	Artery Tibial	GTEx
rs1814323	ADAL	cis	parietal	SCAN
rs1814323	TGM5	cis	lymphoblastoid	seeQTL
rs1814323	TP53BP1	cis	parietal	SCAN
rs1814323	WDR76	cis	parietal	SCAN
rs1814323	ADAL	cis	Adipose Subcutaneous	GTEx
rs1814323	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs1814323	TGM5	cis	multi-tissue	Pritchard
rs1814323	ZSCAN29	cis	Thyroid	GTEx
rs1814323	ADAL	cis	lung	GTEx
rs1814323	TGM7	cis	Esophagus Mucosa	GTEx
rs1814323	ADAL	cis	Nerve Tibial	GTEx
rs1814323	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43551600-43565600	Weak transcription	Right Atrium	heart
2	chr15:43560000-43565400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:43560400-43563600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:43560800-43563800	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:43561400-43568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:43562200-43563400	Enhancers	Fetal Thymus	thymus
7	chr15:43562200-43563600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:43562400-43563400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr15:43562400-43563600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr15:43562600-43563600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:43562600-43563600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr15:43562800-43563400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:43562800-43563400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr15:43562800-43563600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr15:43563000-43563400	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr15:43563000-43563400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:43563200-43563600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:43563200-43563800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:43563200-43566400	Weak transcription	Esophagus	oesophagus

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