Variant report

Variant	rs577289
Chromosome Location	chr15:40208911-40208912
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40208428..40210634-chr15:40211145..40212897,2	K562	blood:
2	chr15:40208007..40210533-chr15:40211533..40213154,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166073	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs1656894	0.85[ASN][1000 genomes]
rs1656895	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1656896	0.94[EUR][1000 genomes]
rs2247984	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412451	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917497	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2934194	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs480095	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486816	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]
rs489424	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494690	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500200	0.88[EUR][1000 genomes]
rs508281	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524240	0.88[EUR][1000 genomes]
rs525910	0.88[EUR][1000 genomes]
rs527610	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs534757	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535407	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs552251	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs562159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.84[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs581233	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030025	0.84[JPT][hapmap]
rs8030687	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs577289	EIF2AK4	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40194600-40211000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:40197200-40210200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:40197400-40209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:40199800-40211800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:40200600-40210400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:40201200-40209800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:40201400-40211600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:40201600-40209800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:40201600-40210200	Weak transcription	HMEC	breast
10	chr15:40201600-40210200	Weak transcription	HUVEC	blood vessel
11	chr15:40201600-40210400	Weak transcription	Aorta	Aorta
12	chr15:40201800-40210200	Weak transcription	HSMMtube	muscle
13	chr15:40201800-40210400	Weak transcription	NHEK	skin
14	chr15:40202000-40209000	Weak transcription	NHLF	lung
15	chr15:40202600-40210400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:40202800-40210200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:40203000-40210400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:40204000-40210000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:40204000-40210200	Weak transcription	NH-A	brain
20	chr15:40207200-40209200	Strong transcription	Osteobl	bone
21	chr15:40207400-40209000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:40207400-40209200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:40207400-40209200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr15:40207400-40210000	Strong transcription	HSMM	muscle
25	chr15:40207600-40209000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:40207600-40209800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:40207800-40209600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:40208200-40209000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:40208200-40209400	Genic enhancers	NHDF-Ad	bronchial
30	chr15:40208200-40210000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:40208400-40209000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr15:40208600-40209000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:40208600-40209200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
34	chr15:40208800-40209000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
35	chr15:40208800-40209000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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