Variant report

Variant	rs17054246
Chromosome Location	chr3:54693752-54693753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10510769	0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs10510770	1.00[ASN][1000 genomes]
rs10510771	1.00[JPT][hapmap]
rs10510772	1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs1130197	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914640	1.00[ASN][1000 genomes]
rs11914780	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914973	1.00[JPT][hapmap]
rs11920788	1.00[JPT][hapmap]
rs11924275	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11925949	1.00[JPT][hapmap]
rs12185982	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1427774	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054227	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17054250	1.00[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054291	1.00[JPT][hapmap]
rs17054293	1.00[JPT][hapmap]
rs17054340	1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs17815617	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17816548	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816566	0.89[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863858	0.89[ASW][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2359857	1.00[JPT][hapmap]
rs28455661	1.00[ASN][1000 genomes]
rs2884808	0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34478567	0.89[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs41381544	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345041	0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4358270	1.00[JPT][hapmap]
rs4386460	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55675480	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772258	1.00[ASN][1000 genomes]
rs56008232	1.00[ASN][1000 genomes]
rs56112781	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56209938	1.00[ASN][1000 genomes]
rs56976748	1.00[ASN][1000 genomes]
rs57924227	1.00[ASN][1000 genomes]
rs58295654	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59004379	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255527	1.00[ASN][1000 genomes]
rs62255533	1.00[ASN][1000 genomes]
rs62255534	1.00[ASN][1000 genomes]
rs62255535	1.00[ASN][1000 genomes]
rs62255536	1.00[ASN][1000 genomes]
rs62255538	1.00[ASN][1000 genomes]
rs6803005	0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72870661	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870676	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870688	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872218	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872226	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872229	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872244	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872259	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872285	1.00[ASN][1000 genomes]
rs72874203	1.00[ASN][1000 genomes]
rs72874204	1.00[ASN][1000 genomes]
rs73068445	1.00[ASN][1000 genomes]
rs737517	1.00[JPT][hapmap]
rs7624695	1.00[JPT][hapmap];1.00[ASN][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17054246	DNAH12	cis	cerebellum	SCAN
rs17054246	ESRG	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54681200-54694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:54684200-54694600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:54685200-54704000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:54686200-54694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54689200-54697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:54691400-54704000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:54693200-54693800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:54693200-54694000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:54693200-54694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:54693200-54694200	Enhancers	Brain Anterior Caudate	brain
11	chr3:54693400-54694000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:54693400-54694000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:54693400-54694000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr3:54693400-54697800	Weak transcription	Right Atrium	heart
15	chr3:54693400-54702400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:54693600-54693800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:54693600-54693800	Enhancers	Fetal Kidney	kidney
18	chr3:54693600-54694000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:54693600-54699200	Enhancers	Fetal Muscle Leg	muscle

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