Variant report

Variant	rs2453533
Chromosome Location	chr15:45641225-45641226
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1049518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519018	1.00[CHB][hapmap]
rs1060896	1.00[CHB][hapmap]
rs1145076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145080	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145084	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145089	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145097	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1153845	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs1153855	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153857	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153862	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632752	1.00[CHB][hapmap]
rs11632778	1.00[CHB][hapmap]
rs11632920	1.00[CHB][hapmap]
rs11636114	0.90[AMR][1000 genomes]
rs11637838	1.00[CHB][hapmap]
rs11637920	1.00[CHB][hapmap]
rs11639420	1.00[CHB][hapmap]
rs11855414	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12904150	1.00[CHB][hapmap]
rs12908818	1.00[CHB][hapmap]
rs12909409	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12910764	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911186	1.00[CHB][hapmap]
rs12913500	0.81[AMR][1000 genomes]
rs12915314	1.00[CHB][hapmap]
rs1346267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1426932	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547487	0.83[AMR][1000 genomes]
rs1617634	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1617984	1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1706770	1.00[CHB][hapmap]
rs1706798	0.80[EUR][1000 genomes]
rs1719231	1.00[CHB][hapmap]
rs1719245	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1719246	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1719250	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs17536527	1.00[CHB][hapmap]
rs2002035	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2015295	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2413768	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413772	1.00[CHB][hapmap]
rs2413774	1.00[CHB][hapmap]
rs2433601	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2433616	0.83[AMR][1000 genomes]
rs2461700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461705	1.00[CHB][hapmap]
rs2467853	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467858	0.89[YRI][hapmap]
rs2467862	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486288	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899375	0.90[AMR][1000 genomes]
rs35861938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493143	1.00[CHB][hapmap]
rs6493144	1.00[CHB][hapmap]
rs6493145	1.00[CHB][hapmap]
rs7165039	1.00[CHB][hapmap]
rs7166580	1.00[CHB][hapmap]
rs7167146	1.00[CHB][hapmap]
rs7171312	1.00[CHB][hapmap]
rs8024620	1.00[CHB][hapmap]
rs8039138	1.00[CHB][hapmap]
rs8039352	1.00[CHB][hapmap]
rs8039354	1.00[CHB][hapmap]
rs8039540	1.00[CHB][hapmap]
rs8043055	0.82[AMR][1000 genomes]
rs872192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921008	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Chronic kidney disease	20383146	GWAS catalog

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2453533	CTD-2651B20.3	cis	lung	GTEx
rs2453533	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2453533	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2453533	CTD-2651B20.3	cis	Thyroid	GTEx
rs2453533	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2453533	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2453533	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2453533	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2453533	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2453533	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2453533	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2453533	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs2453533	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs2453533	CTD-2651B20.4	cis	Artery Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45626000-45652000	Weak transcription	Brain Substantia Nigra	brain
2	chr15:45629800-45642000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:45634600-45651600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:45635200-45641400	Enhancers	HepG2	liver
5	chr15:45635600-45641400	Enhancers	Fetal Intestine Small	intestine
6	chr15:45639200-45664200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:45639600-45642000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:45639600-45661800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:45640200-45642000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:45640400-45641400	Enhancers	Fetal Intestine Large	intestine
11	chr15:45640400-45650000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:45640600-45647600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:45640600-45664200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:45640800-45642000	Weak transcription	Liver	Liver
15	chr15:45640800-45664200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:45641000-45651600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:45641200-45641400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:45641200-45656400	Weak transcription	Gastric	stomach

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