Variant report

Variant	rs12643491
Chromosome Location	chr4:80513804-80513805
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr4:80513698-80514035	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFIC	chr4:80513649-80514269	ECC-1	luminal epithelium:	n/a	n/a
3	USF1	chr4:80513779-80514053	ECC-1	luminal epithelium:	n/a	n/a
4	USF1	chr4:80513759-80513961	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
OR7E94P	TF binding region
ENSG00000251399	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10004226	0.94[ASN][1000 genomes]
rs10022663	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1031004	0.97[ASN][1000 genomes]
rs1031005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098762	0.94[ASN][1000 genomes]
rs11098764	0.94[ASN][1000 genomes]
rs11098766	0.94[ASN][1000 genomes]
rs11098770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1115518	0.90[JPT][hapmap]
rs1115519	0.90[JPT][hapmap]
rs11728755	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736369	0.87[ASN][1000 genomes]
rs11941782	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500146	0.94[ASN][1000 genomes]
rs12501981	0.86[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12507160	0.94[ASN][1000 genomes]
rs12507375	0.94[ASN][1000 genomes]
rs12511646	0.94[ASN][1000 genomes]
rs12643976	0.99[ASN][1000 genomes]
rs13104009	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13112067	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13112577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13124357	0.99[ASN][1000 genomes]
rs13127970	0.91[ASN][1000 genomes]
rs13129838	0.84[ASN][1000 genomes]
rs13142610	0.96[ASN][1000 genomes]
rs13144408	0.82[ASN][1000 genomes]
rs13146986	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1348086	0.96[ASN][1000 genomes]
rs1371989	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371993	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1440852	0.94[ASN][1000 genomes]
rs1440853	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440854	0.94[ASN][1000 genomes]
rs1440864	0.94[ASN][1000 genomes]
rs17003985	0.96[ASN][1000 genomes]
rs1837645	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1837646	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1837647	0.81[ASN][1000 genomes]
rs1866835	0.91[EUR][1000 genomes]
rs1975399	0.94[ASN][1000 genomes]
rs2165386	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165387	0.93[ASN][1000 genomes]
rs2196978	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2582681	0.93[EUR][1000 genomes]
rs2709847	0.93[EUR][1000 genomes]
rs2903640	0.96[ASN][1000 genomes]
rs3109166	0.83[EUR][1000 genomes]
rs35487709	0.96[ASN][1000 genomes]
rs35631270	0.96[ASN][1000 genomes]
rs3943669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4389603	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975056	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975057	0.93[ASN][1000 genomes]
rs4975089	0.90[JPT][hapmap]
rs4975095	0.82[AMR][1000 genomes]
rs4975097	0.95[ASN][1000 genomes]
rs62297619	0.85[EUR][1000 genomes]
rs62297620	0.85[EUR][1000 genomes]
rs6812760	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6850999	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6852514	0.94[ASN][1000 genomes]
rs7667469	0.94[ASN][1000 genomes]
rs7688923	0.85[EUR][1000 genomes]
rs894054	0.93[EUR][1000 genomes]
rs894055	0.93[EUR][1000 genomes]
rs9307545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307551	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968176	0.94[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	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
2	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
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12643491	LINC00989	cis	Muscle Skeletal	GTEx
rs12643491	LINC00989	cis	Whole Blood	GTEx
rs12643491	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs12643491	LINC00989	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80507200-80519400	Weak transcription	Psoas Muscle	Psoas
2	chr4:80510400-80518200	Weak transcription	NHEK	skin
3	chr4:80512200-80514200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:80512600-80514800	Enhancers	Placenta	Placenta
5	chr4:80513000-80514000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links