Variant report

Variant	rs3892125
Chromosome Location	chr2:49272396-49272397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11688474	0.81[EUR][1000 genomes]
rs12617499	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17038141	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134812	0.81[EUR][1000 genomes]
rs2882224	0.81[EUR][1000 genomes]
rs55861243	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60745617	0.81[EUR][1000 genomes]
rs62162077	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62162078	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62162079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62162081	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62162106	0.81[EUR][1000 genomes]
rs73928400	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73931507	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv874007	chr2:49102526-49321164	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv834003	chr2:49131673-49312273	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv581791	chr2:49230413-49296396	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA	n/a	inside rSNPs	diseases
8	nsv874010	chr2:49230413-49393382	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
9	nsv999566	chr2:49247737-49430060	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
10	esv3429664	chr2:49272164-49272641	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:49270800-49272800	Enhancers	Fetal Kidney	kidney
2	chr2:49271400-49272600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:49271400-49272600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:49271400-49273000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:49271600-49272400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:49271600-49272400	Enhancers	Brain Substantia Nigra	brain
7	chr2:49271600-49272400	Enhancers	Ovary	ovary
8	chr2:49271600-49272600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:49271600-49272800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:49271600-49273000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:49271800-49272400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:49271800-49272400	Enhancers	Stomach Smooth Muscle	stomach
13	chr2:49271800-49272600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:49271800-49272800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:49272000-49272600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr2:49272200-49272400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:49272200-49272600	Enhancers	H9 Cell Line	embryonic stem cell

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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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