Variant report

Variant	rs10400901
Chromosome Location	chr15:40883417-40883418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40882574..40885236-chr15:41001374..41003078,2	K562	blood:
2	chr15:40848640..40851135-chr15:40883399..40886206,2	K562	blood:
3	chr15:40876093..40878968-chr15:40880473..40883736,4	K562	blood:
4	chr15:40761695..40764555-chr15:40881844..40883742,2	K562	blood:

Variant related genes	Relation type
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1037445	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400890	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444817	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070282	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070285	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070286	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632061	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11632370	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11852670	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852694	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852828	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855334	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855923	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856802	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858113	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858938	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591207	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902568	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904801	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12905162	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912635	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913697	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914743	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16970851	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1811513	0.81[EUR][1000 genomes]
rs1813898	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1967368	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412531	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412532	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412534	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412544	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2898996	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2924387	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2924388	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3092979	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34845954	0.83[EUR][1000 genomes]
rs35047458	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751652	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751653	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4080706	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4410047	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923876	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4924481	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62019916	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62019918	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6582	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71471881	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169621	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181074	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182530	0.85[EUR][1000 genomes]
rs7183790	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026605	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029384	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8034043	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034048	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036737	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038407	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041534	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs896795	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs976401	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs10400901	C15orf57	cis	Heart Left Ventricle	GTEx
rs10400901	RP11-111A22.1	cis	Artery Aorta	GTEx
rs10400901	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs10400901	RP11-111A22.1	cis	Stomach	GTEx
rs10400901	C15orf57	cis	Artery Tibial	GTEx
rs10400901	C15orf57	cis	Esophagus Mucosa	GTEx
rs10400901	C15orf57	cis	lung	GTEx
rs10400901	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs10400901	C15orf57	cis	Esophagus Muscularis	GTEx
rs10400901	RP11-111A22.1	cis	Artery Tibial	GTEx
rs10400901	C15orf57	cis	Thyroid	GTEx
rs10400901	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs10400901	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs10400901	C15orf57	cis	Adipose Subcutaneous	GTEx
rs10400901	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs10400901	C15orf57	cis	Stomach	GTEx
rs10400901	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs10400901	RP11-111A22.1	cis	lung	GTEx
rs10400901	C15orf57	cis	Muscle Skeletal	GTEx
rs10400901	C15orf57	cis	Artery Aorta	GTEx
rs10400901	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs10400901	C15orf57	cis	Nerve Tibial	GTEx
rs10400901	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:40882000-40886200	Weak transcription	Lung	lung
3	chr15:40882200-40883600	Active TSS	Fetal Intestine Large	intestine
4	chr15:40882200-40883800	Active TSS	HepG2	liver
5	chr15:40882200-40884000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:40882400-40883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40882400-40883600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:40882400-40883600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:40882400-40883800	Enhancers	Stomach Mucosa	stomach
10	chr15:40882400-40885000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:40882400-40886000	Weak transcription	Brain Substantia Nigra	brain
12	chr15:40882400-40886200	Weak transcription	HMEC	breast
13	chr15:40882600-40883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:40882600-40883600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr15:40882600-40884800	Weak transcription	Brain Germinal Matrix	brain
16	chr15:40882600-40884800	Weak transcription	Hela-S3	cervix
17	chr15:40882600-40885000	Weak transcription	NHDF-Ad	bronchial
18	chr15:40882600-40885200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:40882600-40885400	Weak transcription	Fetal Brain Female	brain
20	chr15:40882600-40885600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:40882600-40885800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:40882600-40885800	Weak transcription	Primary T cells from cord blood	blood
23	chr15:40882600-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:40882600-40885800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:40882600-40885800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:40882600-40886000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:40882600-40886000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:40882600-40886000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:40882800-40885200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:40882800-40885400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:40882800-40885400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr15:40882800-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40882800-40885800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr15:40882800-40886000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:40883000-40883600	Active TSS	Fetal Intestine Small	intestine
36	chr15:40883000-40883800	Active TSS	Duodenum Mucosa	Duodenum
37	chr15:40883000-40884000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:40883000-40884000	Enhancers	Fetal Heart	heart
39	chr15:40883000-40884000	Enhancers	Placenta	Placenta
40	chr15:40883000-40885000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:40883000-40885000	Weak transcription	Dnd41	blood
42	chr15:40883000-40885000	Weak transcription	GM12878-XiMat	blood
43	chr15:40883000-40885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:40883000-40885200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:40883000-40885600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:40883000-40885600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:40883000-40885600	Weak transcription	Adipose Nuclei	Adipose
48	chr15:40883000-40885600	Weak transcription	Fetal Kidney	kidney
49	chr15:40883000-40885800	Weak transcription	Fetal Thymus	thymus
50	chr15:40883000-40885800	Weak transcription	Thymus	Thymus

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