Variant report

Variant	rs552701
Chromosome Location	chr15:43613810-43613811
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	chr15:43613133..43615237-chr15:43663798..43666192,2	K562	blood:

Extended variants
information (count: 152 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1079309	0.95[CEU][hapmap]
rs1095386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11070399	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1123947	0.97[ASN][1000 genomes]
rs1133395	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637572	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs11858152	0.94[ASN][1000 genomes]
rs12101673	0.94[ASN][1000 genomes]
rs12102205	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148735	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12323999	0.90[ASN][1000 genomes]
rs12324572	0.97[ASN][1000 genomes]
rs12324584	0.90[ASN][1000 genomes]
rs12905772	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549523	0.97[ASN][1000 genomes]
rs1549525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16957627	0.97[ASN][1000 genomes]
rs16957630	0.97[ASN][1000 genomes]
rs16957632	0.97[ASN][1000 genomes]
rs1814323	0.83[AMR][1000 genomes]
rs1837959	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1837960	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1869258	0.86[CEU][hapmap]
rs2012467	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242068	0.82[ASN][1000 genomes]
rs2242069	0.85[JPT][hapmap]
rs2243434	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2244746	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2244981	0.95[CEU][hapmap]
rs2249952	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2253268	0.95[CEU][hapmap]
rs2264876	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2278856	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2278860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2412778	0.97[ASN][1000 genomes]
rs2412779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2412780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2412781	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412782	0.88[ASN][1000 genomes]
rs2439845	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2444036	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2444251	0.95[CEU][hapmap]
rs2467733	0.87[ASN][1000 genomes]
rs2467737	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2467738	0.91[CEU][hapmap]
rs2467745	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2584700	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2584701	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2584702	0.90[ASN][1000 genomes]
rs2584703	0.85[ASN][1000 genomes]
rs2602141	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28415933	0.97[ASN][1000 genomes]
rs28461955	0.97[ASN][1000 genomes]
rs28653441	0.93[ASN][1000 genomes]
rs28702649	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28729853	0.93[ASN][1000 genomes]
rs2899082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213990	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3213991	0.81[CHB][hapmap];0.95[ASN][1000 genomes]
rs3742969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3742971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3809482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4296223	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4401024	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4583210	0.97[ASN][1000 genomes]
rs475227	0.81[AMR][1000 genomes]
rs478028	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478104	0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs484029	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs484846	0.95[ASN][1000 genomes]
rs485148	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488756	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs491800	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs493377	0.95[CEU][hapmap]
rs493444	0.83[AMR][1000 genomes]
rs498837	0.95[ASN][1000 genomes]
rs499035	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501884	0.83[AMR][1000 genomes]
rs504417	0.83[AMR][1000 genomes]
rs505249	0.83[AMR][1000 genomes]
rs506120	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs507178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509306	0.83[EUR][1000 genomes]
rs510108	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511673	0.98[ASN][1000 genomes]
rs512431	0.81[AMR][1000 genomes]
rs512628	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513970	0.84[AMR][1000 genomes]
rs523156	0.82[CEU][hapmap]
rs523737	0.83[AMR][1000 genomes]
rs524527	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs526450	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs528517	1.00[ASN][1000 genomes]
rs529611	0.86[CEU][hapmap]
rs530188	0.83[AMR][1000 genomes]
rs536313	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs538238	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs540031	1.00[ASN][1000 genomes]
rs542898	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs554001	0.83[AMR][1000 genomes]
rs556851	0.83[AMR][1000 genomes]
rs560134	0.83[AMR][1000 genomes]
rs567357	0.83[AMR][1000 genomes]
rs572959	0.83[AMR][1000 genomes]
rs573615	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576557	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493081	0.96[ASN][1000 genomes]
rs6493082	0.97[ASN][1000 genomes]
rs6493083	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493084	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6493086	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493087	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6493088	0.95[ASN][1000 genomes]
rs689693	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689767	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs690012	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs690276	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690367	0.95[CEU][hapmap]
rs690512	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs693510	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs694725	0.95[CEU][hapmap]
rs7163245	0.93[ASN][1000 genomes]
rs7163288	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7165471	0.97[ASN][1000 genomes]
rs7166812	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7167882	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168940	0.94[ASN][1000 genomes]
rs7170152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7172374	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175434	0.95[ASN][1000 genomes]
rs7176849	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs8033714	0.93[ASN][1000 genomes]
rs8039638	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8041132	0.97[ASN][1000 genomes]
rs8042688	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs825739	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs825740	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs884704	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs933941	0.97[ASN][1000 genomes]
rs956391	0.99[ASN][1000 genomes]
rs9920879	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999026	0.88[ASN][1000 genomes]
rs999047	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs552701	AC011330.5	cis	Artery Tibial	GTEx
rs552701	TGM7	cis	Esophagus Mucosa	GTEx
rs552701	ZSCAN29	cis	Thyroid	GTEx
rs552701	ADAL	cis	Nerve Tibial	GTEx
rs552701	TGM5	cis	multi-tissue	Pritchard
rs552701	ADAL	cis	lung	GTEx
rs552701	ZSCAN29	cis	multi-tissue	Pritchard
rs552701	ELL3	cis	multi-tissue	Pritchard
rs552701	TGM5	Cis_1M	lymphoblastoid	RTeQTL
rs552701	AC011330.5	cis	Thyroid	GTEx
rs552701	STRCP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43609000-43620200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:43611600-43620200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:43613000-43620600	Weak transcription	Right Atrium	heart
4	chr15:43613600-43620200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links