Variant report

Variant	rs62255538
Chromosome Location	chr3:54671419-54671420
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10510769	1.00[ASN][1000 genomes]
rs10510770	1.00[ASN][1000 genomes]
rs10510772	1.00[ASN][1000 genomes]
rs1130197	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914640	1.00[ASN][1000 genomes]
rs11914780	1.00[ASN][1000 genomes]
rs11924275	1.00[ASN][1000 genomes]
rs12185982	1.00[ASN][1000 genomes]
rs1427774	1.00[ASN][1000 genomes]
rs17054227	1.00[ASN][1000 genomes]
rs17054246	1.00[ASN][1000 genomes]
rs17054250	1.00[ASN][1000 genomes]
rs17054340	1.00[ASN][1000 genomes]
rs17815617	1.00[ASN][1000 genomes]
rs17816548	1.00[ASN][1000 genomes]
rs17816566	1.00[ASN][1000 genomes]
rs1863858	1.00[ASN][1000 genomes]
rs28455661	1.00[ASN][1000 genomes]
rs2884808	1.00[ASN][1000 genomes]
rs34478567	1.00[ASN][1000 genomes]
rs41381544	1.00[ASN][1000 genomes]
rs4345041	1.00[ASN][1000 genomes]
rs4386460	1.00[ASN][1000 genomes]
rs55675480	1.00[ASN][1000 genomes]
rs55772258	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779022	0.82[EUR][1000 genomes]
rs56008232	1.00[ASN][1000 genomes]
rs56091855	0.82[EUR][1000 genomes]
rs56112781	1.00[ASN][1000 genomes]
rs56209938	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260111	0.82[EUR][1000 genomes]
rs56356828	0.81[EUR][1000 genomes]
rs56976748	1.00[ASN][1000 genomes]
rs57924227	1.00[ASN][1000 genomes]
rs58295654	1.00[ASN][1000 genomes]
rs59004379	1.00[ASN][1000 genomes]
rs62255527	1.00[ASN][1000 genomes]
rs62255532	0.82[EUR][1000 genomes]
rs62255533	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255534	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255535	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255536	1.00[ASN][1000 genomes]
rs6803005	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870661	1.00[ASN][1000 genomes]
rs72870676	1.00[ASN][1000 genomes]
rs72870688	1.00[ASN][1000 genomes]
rs72872218	1.00[ASN][1000 genomes]
rs72872226	1.00[ASN][1000 genomes]
rs72872229	1.00[ASN][1000 genomes]
rs72872244	1.00[ASN][1000 genomes]
rs72872259	1.00[ASN][1000 genomes]
rs72872285	1.00[ASN][1000 genomes]
rs72874203	1.00[ASN][1000 genomes]
rs72874204	1.00[ASN][1000 genomes]
rs73068445	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624695	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3335458	chr3:54668624-54674022	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62255538	ZNF12	trans	lymphoblastoid	RTeQTL
rs62255538	TNFRSF17	trans	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54665200-54672800	Weak transcription	Right Atrium	heart
3	chr3:54667800-54672200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
4	chr3:54667800-54672400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr3:54668400-54671600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:54668400-54674400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:54668400-54674400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:54669000-54674400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:54669400-54672200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
10	chr3:54669400-54674200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:54669800-54672000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
12	chr3:54669800-54672200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
13	chr3:54669800-54673000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
14	chr3:54669800-54673000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
15	chr3:54669800-54674200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:54670800-54672200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
17	chr3:54671400-54674400	Active TSS	H9 Cell Line	embryonic stem cell

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