Variant report

Variant	rs1689605
Chromosome Location	chr15:40215061-40215062
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr15:40214783-40215092	GM12878	blood:	n/a	chr15:40214928-40214939 chr15:40214910-40214921
2	EBF1	chr15:40214706-40215123	GM12878	blood:	n/a	chr15:40214928-40214939 chr15:40214910-40214921
3	KAP1	chr15:40214767-40215265	U2OS	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40214834..40219458-chr15:40222098..40228403,10	K562	blood:
2	chr15:40214696..40216721-chr15:40223722..40226672,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2AK4-1	chr15:40214988-40217099	ENSG00000246863
2	lnc-EIF2AK4-1	chr15:40214988-40217139	XLOC_011218
3	lnc-EIF2AK4-1	chr15:40214988-40218031	XLOC_011218
4	lnc-EIF2AK4-1	chr15:40214988-40218031	XLOC_011218
5	lnc-EIF2AK4-1	chr15:40214988-40217100	ENSG00000246863.2
6	lnc-EIF2AK4-1	chr15:40213271-40218081	ENSG00000246863.2

No data

Variant related genes	Relation type
GPR176	TF binding region
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10459608	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1436278	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16970030	0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs16970033	0.94[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs16970098	0.80[CHB][hapmap]
rs16970132	0.85[GIH][hapmap];0.88[JPT][hapmap]
rs16970168	0.81[JPT][hapmap]
rs2196470	0.87[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2279580	0.81[JPT][hapmap]
rs2291623	0.81[JPT][hapmap]
rs2307105	0.88[CHD][hapmap];0.85[GIH][hapmap]
rs2307107	0.82[JPT][hapmap]
rs2898974	0.81[JPT][hapmap]
rs35390951	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4566130	0.94[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs503671	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs510949	0.88[CHD][hapmap];0.85[GIH][hapmap]
rs514152	0.88[CHD][hapmap];0.85[GIH][hapmap]
rs66690776	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165105	0.85[GIH][hapmap];0.88[JPT][hapmap]
rs7170569	0.80[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7174767	0.80[CHD][hapmap];0.85[GIH][hapmap]
rs72729459	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72729462	0.82[ASN][1000 genomes]

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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40213600-40217600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40213600-40225000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:40213600-40225400	Weak transcription	Pancreas	Pancrea
4	chr15:40213800-40215200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:40213800-40215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:40213800-40215200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:40213800-40215200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:40213800-40215200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:40213800-40215200	Enhancers	NHDF-Ad	bronchial
10	chr15:40213800-40215200	Enhancers	Osteobl	bone
11	chr15:40213800-40216600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:40213800-40217400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:40213800-40217400	Weak transcription	HSMMtube	muscle
14	chr15:40213800-40217400	Weak transcription	HUVEC	blood vessel
15	chr15:40213800-40217400	Weak transcription	NH-A	brain
16	chr15:40213800-40217600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:40213800-40217800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:40213800-40225800	Weak transcription	Right Atrium	heart
19	chr15:40214000-40215400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr15:40214000-40216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:40214000-40216800	Weak transcription	K562	blood
22	chr15:40214000-40217400	Weak transcription	Hela-S3	cervix
23	chr15:40214400-40215200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr15:40214400-40215200	Enhancers	HMEC	breast
25	chr15:40214400-40215200	Enhancers	HSMM	muscle
26	chr15:40214400-40215200	Enhancers	NHLF	lung
27	chr15:40214400-40215400	Enhancers	NHEK	skin
28	chr15:40214400-40215600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:40214600-40215200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:40214600-40215200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:40214600-40215200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:40214800-40215200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr15:40214800-40215200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr15:40214800-40215200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr15:40214800-40215200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:40214800-40215200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:40214800-40215200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:40214800-40215600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:40215000-40215400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:40215000-40217400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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