Variant report

Variant	rs486816
Chromosome Location	chr15:40225465-40225466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr15:40225454-40227400	IMR90	lung:	n/a	n/a
2	POLR2A	chr15:40225370-40226697	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:40211846..40214390-chr15:40224576..40226655,2	K562	blood:
2	chr15:40214834..40219458-chr15:40222098..40228403,10	K562	blood:
3	chr15:40209081..40211622-chr15:40223398..40225588,2	K562	blood:
4	chr15:40093040..40094841-chr15:40224572..40226141,2	K562	blood:
5	chr15:40214696..40216721-chr15:40223722..40226672,2	MCF-7	breast:
6	chr15:40211366..40214080-chr15:40223428..40228644,6	MCF-7	breast:
7	chr15:40224751..40226290-chr15:40266670..40268838,2	MCF-7	breast:

No data

Variant related genes	Relation type
EIF2AK4	TF binding region
ENSG00000246863	Chromatin interaction
ENSG00000259580	Chromatin interaction
ENSG00000166073	Chromatin interaction
ENSG00000200305	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10518676	0.84[JPT][hapmap]
rs10851392	0.82[JPT][hapmap]
rs11633416	0.84[JPT][hapmap]
rs12324733	0.82[JPT][hapmap]
rs12439335	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs1656894	0.87[ASN][1000 genomes]
rs1656895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656896	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2247984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412451	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917497	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934194	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs480095	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489424	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500200	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508281	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518770	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524240	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs525910	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs527610	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534757	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535407	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs552251	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs562159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs581233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030025	0.84[JPT][hapmap]
rs8030687	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs486816	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs486816	FAM98B	cis	parietal	SCAN
rs486816	EIF2AK4	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40213800-40225800	Weak transcription	Right Atrium	heart
2	chr15:40215200-40226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:40215600-40225800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:40224200-40225600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr15:40224200-40225600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:40224200-40226000	Weak transcription	Fetal Heart	heart
7	chr15:40224800-40225800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:40224800-40225800	Enhancers	NHLF	lung
9	chr15:40224800-40226800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:40224800-40227800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:40225000-40225600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr15:40225000-40225600	Enhancers	Dnd41	blood
13	chr15:40225000-40225600	Flanking Active TSS	Hela-S3	cervix
14	chr15:40225000-40225800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr15:40225000-40225800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:40225000-40225800	Enhancers	Psoas Muscle	Psoas
17	chr15:40225200-40225600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:40225200-40225600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr15:40225200-40225600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:40225200-40225600	Flanking Active TSS	HMEC	breast
21	chr15:40225200-40225800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr15:40225200-40225800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr15:40225200-40225800	Enhancers	HUVEC	blood vessel
24	chr15:40225200-40226000	Enhancers	Fetal Brain Male	brain
25	chr15:40225200-40226200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:40225200-40227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr15:40225400-40225600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:40225400-40225600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr15:40225400-40225600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr15:40225400-40225600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40225400-40225600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:40225400-40225600	Enhancers	Spleen	Spleen
33	chr15:40225400-40225600	Bivalent Enhancer	HepG2	liver
34	chr15:40225400-40225600	Flanking Active TSS	NHEK	skin
35	chr15:40225400-40225600	Flanking Active TSS	Osteobl	bone
36	chr15:40225400-40225800	Enhancers	Primary B cells from cord blood	blood
37	chr15:40225400-40225800	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:40225400-40225800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:40225400-40225800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr15:40225400-40225800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:40225400-40225800	Enhancers	Brain Germinal Matrix	brain
42	chr15:40225400-40225800	Enhancers	Fetal Thymus	thymus
43	chr15:40225400-40225800	Enhancers	Pancreas	Pancrea
44	chr15:40225400-40225800	Weak transcription	Small Intestine	intestine
45	chr15:40225400-40225800	Enhancers	GM12878-XiMat	blood
46	chr15:40225400-40225800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr15:40225400-40226000	Weak transcription	NHDF-Ad	bronchial
48	chr15:40225400-40226400	Active TSS	Colonic Mucosa	Colon
49	chr15:40225400-40226600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:40225400-40226600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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