Variant report

Variant	rs1435809
Chromosome Location	chr2:52039485-52039486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10192876	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11125388	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1188252	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010634	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347497	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1369672	0.85[EUR][1000 genomes]
rs1369673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550101	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561923	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7591096	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7594115	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs979467	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs988518	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs988519	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv874079	chr2:51935797-52083566	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874080	chr2:51946163-52068507	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581914	chr2:51959258-52074452	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv431047	chr2:51961737-52263543	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv874081	chr2:51975932-52062108	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013553	chr2:52010500-52471153	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv535712	chr2:52010500-52471153	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv874083	chr2:52024350-52094039	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv874084	chr2:52025123-52062108	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv874085	chr2:52025123-52068507	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv874086	chr2:52025123-52094467	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv874087	chr2:52030983-52060125	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv581915	chr2:52030983-52066351	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1435809	MTIF2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52038400-52039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr2:52038800-52040800	Enhancers	Osteobl	bone
3	chr2:52039000-52041200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr2:52039200-52041000	Enhancers	HMEC	breast
5	chr2:52039200-52041000	Enhancers	NH-A	brain
6	chr2:52039200-52041200	Enhancers	NHDF-Ad	bronchial
7	chr2:52039200-52041600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:52039200-52042400	Enhancers	HUVEC	blood vessel
9	chr2:52039400-52039600	Enhancers	Hela-S3	cervix
10	chr2:52039400-52039800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:52039400-52040400	Enhancers	NHLF	lung
12	chr2:52039400-52041000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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