Variant report

Variant	rs4925026
Chromosome Location	chr17:19546100-19546101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1004490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1004491	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1034897	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204407	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11650399	0.86[CHD][hapmap]
rs12601634	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604069	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12940877	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945345	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16960251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2120271	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672254	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891951	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34242564	0.82[EUR][1000 genomes]
rs34653191	0.80[EUR][1000 genomes]
rs35364675	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3752046	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786038	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4244600	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4621031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646800	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924788	0.92[EUR][1000 genomes]
rs4924791	0.82[AMR][1000 genomes]
rs4925000	0.82[EUR][1000 genomes]
rs4925001	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925002	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925037	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925038	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925040	0.81[AMR][1000 genomes]
rs4925041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56262978	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58835440	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58970893	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61631401	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67870359	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68066777	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216938	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73981559	0.92[EUR][1000 genomes]
rs7502080	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs758427	0.81[GIH][hapmap]
rs962801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs968012	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9902636	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9909886	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9914765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1059195	chr17:19484803-19547972	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv574577	chr17:19505984-19546100	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv543256	chr17:19515267-19547972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv574579	chr17:19515695-19546100	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4925026	ALDH3A2	cis	parietal	SCAN
rs4925026	MFAP4	cis	parietal	SCAN
rs4925026	FLJ10847	cis	multi-tissue	Pritchard
rs4925026	ALDH3A2	cis	multi-tissue	Pritchard
rs4925026	TOM1L2	cis	parietal	SCAN
rs4925026	ALDH3A2	cis	lymphoblastoid	seeQTL
rs4925026	ALDH3A2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19538000-19549400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:19544400-19546400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr17:19544400-19547000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr17:19544800-19546200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr17:19545000-19546200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr17:19545000-19546200	Enhancers	NHEK	skin
7	chr17:19545000-19546800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr17:19545000-19548800	Enhancers	Hela-S3	cervix
9	chr17:19545200-19546200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:19545200-19546200	Flanking Active TSS	Liver	Liver
11	chr17:19545200-19546400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr17:19545200-19547200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr17:19545200-19548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:19545400-19546200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr17:19545400-19546200	Enhancers	A549	lung
16	chr17:19545400-19549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:19545600-19550400	Enhancers	HepG2	liver
18	chr17:19545800-19547000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr17:19545800-19550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:19546000-19546200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr17:19546000-19549800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links