Variant report

Variant	rs1364989
Chromosome Location	chr4:55011769-55011770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55011296..55011796-chr9:131873114..131873945,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000095321	Chromatin interaction
ENSG00000119383	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1017280	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11725470	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12506808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12507253	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12510014	0.87[EUR][1000 genomes]
rs12512002	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12648383	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13112338	0.87[EUR][1000 genomes]
rs13131948	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148062	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34372785	0.84[EUR][1000 genomes]
rs34797391	0.87[EUR][1000 genomes]
rs35422368	0.87[EUR][1000 genomes]
rs35511042	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35638196	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs36035401	0.85[EUR][1000 genomes]
rs41386153	0.87[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs4864853	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554148	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs6811208	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811249	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6817230	0.84[EUR][1000 genomes]
rs6842144	0.95[EUR][1000 genomes]
rs6842584	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs6850083	0.95[EUR][1000 genomes]
rs71597863	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71597864	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71597865	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7659453	0.88[EUR][1000 genomes]
rs7667373	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676108	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7677077	0.88[EUR][1000 genomes]
rs7677087	0.88[EUR][1000 genomes]
rs7695934	0.84[EUR][1000 genomes]
rs929967	0.85[EUR][1000 genomes]
rs929968	0.86[EUR][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	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv879020	chr4:54986912-55064573	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lupus nephritis in systemic lupus erythematosus	24925725	GWAS catalog

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55010000-55011800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr4:55010000-55012400	Enhancers	Fetal Thymus	thymus
3	chr4:55010000-55012600	Enhancers	Thymus	Thymus
4	chr4:55010400-55012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:55010400-55012600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:55010600-55011800	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:55010800-55012400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:55011000-55011800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:55011200-55011800	Enhancers	HSMM	muscle
10	chr4:55011600-55015600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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