Variant report

Variant	rs10400890
Chromosome Location	chr15:40883101-40883102
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr15:40882911-40883228	K562	blood:	n/a	n/a
2	IRF1	chr15:40882981-40883175	K562	blood:	n/a	n/a
3	GATA3	chr15:40882946-40883238	T-47D	breast:	n/a	n/a
4	IRF1	chr15:40882911-40883262	K562	blood:	n/a	n/a
5	GTF3C2	chr15:40881970-40883215	K562	blood:	n/a	n/a
6	SPI1	chr15:40882996-40883170	K562	blood:	n/a	n/a
7	RCOR1	chr15:40883079-40883178	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1037445	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400901	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444817	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070277	0.82[EUR][1000 genomes]
rs11070282	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070285	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070286	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632061	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11632370	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11638742	0.82[EUR][1000 genomes]
rs11639464	0.80[EUR][1000 genomes]
rs11852670	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852694	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852828	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854986	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855334	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855923	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856802	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858113	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591207	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594548	0.82[EUR][1000 genomes]
rs12595610	0.82[EUR][1000 genomes]
rs12902568	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904801	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12905162	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912635	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913697	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914743	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16970851	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1811513	0.84[EUR][1000 genomes]
rs1813898	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1967368	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412531	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412534	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412544	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2898996	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2924387	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2924388	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2959536	0.82[EUR][1000 genomes]
rs3092979	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34845954	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35047458	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751652	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751653	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4080706	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4410047	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923875	0.82[EUR][1000 genomes]
rs4923876	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4924478	0.82[EUR][1000 genomes]
rs4924479	0.82[EUR][1000 genomes]
rs4924480	0.82[EUR][1000 genomes]
rs4924481	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62019916	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62019918	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492951	0.82[EUR][1000 genomes]
rs6582	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71471881	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169621	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181074	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182530	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7183790	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7494968	0.81[EUR][1000 genomes]
rs8026605	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029384	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8034043	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034048	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036737	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038407	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041534	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs896795	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs976401	0.84[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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs10400890	C15orf57	cis	Esophagus Muscularis	GTEx
rs10400890	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs10400890	C15orf57	cis	Artery Tibial	GTEx
rs10400890	CCDC32	cis	multi-tissue	Pritchard
rs10400890	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs10400890	C15orf57	cis	lung	GTEx
rs10400890	RP11-111A22.1	cis	lung	GTEx
rs10400890	C15orf57	cis	Stomach	GTEx
rs10400890	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs10400890	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs10400890	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs10400890	C15orf57	cis	Muscle Skeletal	GTEx
rs10400890	RP11-111A22.1	cis	Artery Tibial	GTEx
rs10400890	C15orf57	cis	Artery Aorta	GTEx
rs10400890	ZFYVE19	cis	multi-tissue	Pritchard
rs10400890	C15orf57	cis	Heart Left Ventricle	GTEx
rs10400890	RP11-111A22.1	cis	Stomach	GTEx
rs10400890	C15orf57	cis	Adipose Subcutaneous	GTEx
rs10400890	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs10400890	C15orf57	cis	Esophagus Mucosa	GTEx
rs10400890	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs10400890	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs10400890	C15orf57	cis	Nerve Tibial	GTEx
rs10400890	RP11-111A22.1	cis	Artery Aorta	GTEx
rs10400890	C15orf57	cis	Thyroid	GTEx

Chromatin state (count:78 , 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	chr15:40881800-40883200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:40881800-40883200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:40881800-40883200	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:40882000-40883200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr15:40882000-40883200	Active TSS	Ovary	ovary
7	chr15:40882000-40886200	Weak transcription	Lung	lung
8	chr15:40882200-40883200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:40882200-40883200	Active TSS	Aorta	Aorta
10	chr15:40882200-40883200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr15:40882200-40883400	Active TSS	Fetal Stomach	stomach
12	chr15:40882200-40883400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr15:40882200-40883400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr15:40882200-40883400	Active TSS	Right Atrium	heart
15	chr15:40882200-40883600	Active TSS	Fetal Intestine Large	intestine
16	chr15:40882200-40883800	Active TSS	HepG2	liver
17	chr15:40882200-40884000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:40882400-40883400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:40882400-40883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:40882400-40883600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:40882400-40883600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:40882400-40883800	Enhancers	Stomach Mucosa	stomach
23	chr15:40882400-40885000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:40882400-40886000	Weak transcription	Brain Substantia Nigra	brain
25	chr15:40882400-40886200	Weak transcription	HMEC	breast
26	chr15:40882600-40883200	Flanking Active TSS	K562	blood
27	chr15:40882600-40883400	Enhancers	Primary B cells from cord blood	blood
28	chr15:40882600-40883400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:40882600-40883400	Weak transcription	A549	lung
30	chr15:40882600-40883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:40882600-40883600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:40882600-40884800	Weak transcription	Brain Germinal Matrix	brain
33	chr15:40882600-40884800	Weak transcription	Hela-S3	cervix
34	chr15:40882600-40885000	Weak transcription	NHDF-Ad	bronchial
35	chr15:40882600-40885200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:40882600-40885400	Weak transcription	Fetal Brain Female	brain
37	chr15:40882600-40885600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:40882600-40885800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:40882600-40885800	Weak transcription	Primary T cells from cord blood	blood
40	chr15:40882600-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:40882600-40885800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:40882600-40885800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:40882600-40886000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:40882600-40886000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:40882600-40886000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:40882800-40883200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:40882800-40885200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:40882800-40885400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:40882800-40885400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:40882800-40885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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