Variant report

Variant	rs13129838
Chromosome Location	chr4:80508788-80508789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10004226	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10022663	0.87[ASN][1000 genomes]
rs1031004	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1031005	0.84[ASN][1000 genomes]
rs11098762	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098764	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098766	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098770	0.84[ASN][1000 genomes]
rs11728755	0.81[ASN][1000 genomes]
rs11736369	0.82[ASN][1000 genomes]
rs11941782	0.84[ASN][1000 genomes]
rs12500146	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12501981	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12507160	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12507375	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12511646	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12643491	0.84[ASN][1000 genomes]
rs12643976	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13104009	0.84[ASN][1000 genomes]
rs13112067	0.84[ASN][1000 genomes]
rs13112577	0.84[ASN][1000 genomes]
rs13124357	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13127970	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13142610	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13146986	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1348086	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1371989	0.84[ASN][1000 genomes]
rs1371993	0.84[ASN][1000 genomes]
rs1440852	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1440853	0.87[ASN][1000 genomes]
rs1440854	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1440864	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17003985	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837645	0.84[ASN][1000 genomes]
rs1837646	0.84[ASN][1000 genomes]
rs1975399	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2165386	0.87[ASN][1000 genomes]
rs2165387	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2903640	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35487709	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35631270	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3943669	0.84[ASN][1000 genomes]
rs4389603	0.87[ASN][1000 genomes]
rs4975056	0.84[ASN][1000 genomes]
rs4975057	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975097	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6812760	0.84[ASN][1000 genomes]
rs6850999	0.87[ASN][1000 genomes]
rs6852514	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7667469	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9307545	0.84[ASN][1000 genomes]
rs9307551	0.84[ASN][1000 genomes]
rs968176	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999174	chr4:80212935-80512356	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv966289	chr4:80506013-80509660	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13129838	LINC00989	cis	Whole Blood	GTEx
rs13129838	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs13129838	LINC00989	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80507000-80510000	Weak transcription	Placenta	Placenta
2	chr4:80507000-80511600	Weak transcription	Fetal Heart	heart
3	chr4:80507200-80519400	Weak transcription	Psoas Muscle	Psoas
4	chr4:80507400-80510200	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links