Variant report

Variant	rs2467853
Chromosome Location	chr15:45698793-45698794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45457789..45460616-chr15:45698147..45700403,2	K562	blood:
2	chr15:45698341..45700886-chr15:45711508..45714257,3	K562	blood:
3	chr15:45698341..45701753-chr15:45711661..45714257,4	K562	blood:
4	chr15:45698135..45700009-chr15:45705389..45707645,2	K562	blood:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1049518	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145076	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145077	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145086	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145089	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145093	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145097	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153845	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1153855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153860	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153862	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636114	0.88[AMR][1000 genomes]
rs11855414	0.90[AMR][1000 genomes]
rs12909409	0.90[AMR][1000 genomes]
rs12910764	0.90[AMR][1000 genomes]
rs1346267	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547487	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1617634	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1617984	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1719245	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1719246	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719250	0.91[CEU][hapmap]
rs2002035	0.86[AMR][1000 genomes]
rs2015295	0.85[AMR][1000 genomes]
rs2433601	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2433616	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2453533	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461700	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461701	0.80[AFR][1000 genomes]
rs2467858	0.80[AFR][1000 genomes]
rs2467862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467865	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486274	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899375	0.88[AMR][1000 genomes]
rs35861938	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872192	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9921008	0.86[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
Renal function and chronic kidney disease	19430482	GWAS catalog

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2467853	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2467853	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2467853	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs2467853	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2467853	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2467853	CTD-2651B20.3	cis	lung	GTEx
rs2467853	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2467853	CTD-2651B20.3	cis	Thyroid	GTEx
rs2467853	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2467853	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2467853	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2467853	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2467853	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2467853	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45696000-45699200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:45696000-45699200	Weak transcription	Esophagus	oesophagus
3	chr15:45696000-45699400	Weak transcription	Gastric	stomach
4	chr15:45696000-45703000	Weak transcription	Lung	lung
5	chr15:45696000-45703200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:45696000-45703200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:45696200-45700800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:45696200-45703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:45696200-45707400	Weak transcription	Small Intestine	intestine
10	chr15:45696200-45712800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:45696400-45699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45696400-45699200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:45696400-45703400	Weak transcription	Aorta	Aorta
14	chr15:45696600-45698800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:45696600-45699000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:45696600-45699200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:45696600-45699200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:45696600-45699200	Weak transcription	NHDF-Ad	bronchial
19	chr15:45696600-45700200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:45696600-45703200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:45696600-45711000	Weak transcription	Stomach Mucosa	stomach
22	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:45696800-45699000	Weak transcription	A549	lung
25	chr15:45696800-45699200	Weak transcription	Fetal Heart	heart
26	chr15:45696800-45699200	Weak transcription	Fetal Stomach	stomach
27	chr15:45696800-45699200	Weak transcription	NHLF	lung
28	chr15:45696800-45706000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:45697000-45699000	Weak transcription	Psoas Muscle	Psoas
31	chr15:45697000-45699000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:45697000-45699200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:45697000-45699200	Weak transcription	Colonic Mucosa	Colon
34	chr15:45697000-45699200	Weak transcription	Pancreas	Pancrea
35	chr15:45697000-45699200	Weak transcription	Thymus	Thymus
36	chr15:45697000-45699200	Weak transcription	NHEK	skin
37	chr15:45697000-45699400	Genic enhancers	Dnd41	blood
38	chr15:45697000-45700800	Weak transcription	Right Ventricle	heart
39	chr15:45697000-45702600	Weak transcription	Spleen	Spleen
40	chr15:45697000-45711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:45697200-45699400	Strong transcription	Fetal Kidney	kidney
43	chr15:45697200-45703400	Strong transcription	HSMM	muscle
44	chr15:45697200-45706000	Strong transcription	Brain Substantia Nigra	brain
45	chr15:45697200-45706400	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:45697200-45712400	Strong transcription	Placenta	Placenta
47	chr15:45697200-45713800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr15:45697200-45714200	Strong transcription	Osteobl	bone
49	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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