Variant report

Variant	rs11098770
Chromosome Location	chr4:80520004-80520005
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:80516564..80518189-chr4:80518557..80520658,2	K562	blood:

Variant related genes	Relation type
ENSG00000251399	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10004226	0.94[ASN][1000 genomes]
rs10022663	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1031004	0.99[ASN][1000 genomes]
rs1031005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098762	0.94[ASN][1000 genomes]
rs11098764	0.94[ASN][1000 genomes]
rs11098766	0.94[ASN][1000 genomes]
rs1115518	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1115519	0.90[JPT][hapmap]
rs11728755	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11736369	0.87[ASN][1000 genomes]
rs11941782	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12500146	0.94[ASN][1000 genomes]
rs12501981	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12507160	0.94[ASN][1000 genomes]
rs12507375	0.94[ASN][1000 genomes]
rs12511646	0.94[ASN][1000 genomes]
rs12643491	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]
rs12643976	0.98[ASN][1000 genomes]
rs13104009	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112067	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13112577	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13124357	0.98[ASN][1000 genomes]
rs13127970	0.90[ASN][1000 genomes]
rs13129838	0.84[ASN][1000 genomes]
rs13142610	1.00[ASN][1000 genomes]
rs13144408	0.81[ASN][1000 genomes]
rs13146986	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1348086	1.00[ASN][1000 genomes]
rs1371989	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371993	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1440852	0.94[ASN][1000 genomes]
rs1440853	0.86[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	1.00[ASN][1000 genomes]
rs1837645	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837646	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1866835	0.91[EUR][1000 genomes]
rs1975399	0.94[ASN][1000 genomes]
rs2165386	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165387	0.92[ASN][1000 genomes]
rs2196978	0.91[ASN][1000 genomes]
rs2582681	0.93[EUR][1000 genomes]
rs2709847	0.93[EUR][1000 genomes]
rs2903640	0.99[ASN][1000 genomes]
rs3109166	0.83[EUR][1000 genomes]
rs35487709	1.00[ASN][1000 genomes]
rs35631270	1.00[ASN][1000 genomes]
rs3943669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4389603	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975056	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975057	0.92[ASN][1000 genomes]
rs4975089	0.90[JPT][hapmap]
rs4975097	0.99[ASN][1000 genomes]
rs62297619	0.85[EUR][1000 genomes]
rs62297620	0.85[EUR][1000 genomes]
rs6812760	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850999	0.86[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307551	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11098770	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs11098770	LINC00989	cis	Whole Blood	GTEx
rs11098770	LINC00989	cis	Adipose Subcutaneous	GTEx
rs11098770	PPEF2	cis	parietal	SCAN
rs11098770	LINC00989	cis	Muscle Skeletal	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80518600-80520200	Enhancers	Primary B cells from peripheral blood	blood
2	chr4:80518600-80520400	Enhancers	K562	blood
3	chr4:80519200-80520800	Enhancers	Primary B cells from cord blood	blood
4	chr4:80519200-80521000	Enhancers	Colon Smooth Muscle	Colon
5	chr4:80519200-80521000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr4:80519200-80521200	Enhancers	Rectal Smooth Muscle	rectum
7	chr4:80519400-80520200	Enhancers	Left Ventricle	heart
8	chr4:80519400-80521800	Enhancers	Primary T cells from cord blood	blood
9	chr4:80519600-80520200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:80519600-80520800	Weak transcription	Right Atrium	heart
11	chr4:80519800-80520200	Flanking Active TSS	Aorta	Aorta
12	chr4:80519800-80520400	Active TSS	Stomach Smooth Muscle	stomach
13	chr4:80519800-80521000	Enhancers	Fetal Brain Male	brain
14	chr4:80520000-80520800	Weak transcription	Psoas Muscle	Psoas
15	chr4:80520000-80521000	Enhancers	Fetal Brain Female	brain

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