Variant report

Variant	rs17624325
Chromosome Location	chr3:60595986-60595987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13060659	0.93[CHB][hapmap]
rs13080485	0.93[CHB][hapmap]
rs17624439	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17624499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs17670088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17670154	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670198	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34600947	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap]
rs715382	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap]
rs7638130	0.93[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs17624325	DNASE1L3	cis	parietal	SCAN
rs17624325	RPP14	cis	cerebellum	SCAN
rs17624325	DNASE1L3	cis	cerebellum	SCAN
rs17624325	FAM3D	cis	cerebellum	SCAN
rs17624325	DNAH12	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60594800-60596800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:60595200-60596200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:60595200-60596600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:60595200-60597000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:60595400-60596800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:60595400-60596800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:60595400-60597000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:60595400-60597000	Enhancers	NHLF	lung
9	chr3:60595400-60597000	Enhancers	Osteobl	bone
10	chr3:60595600-60596000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:60595600-60596200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:60595600-60596400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr3:60595600-60596600	Weak transcription	Fetal Stomach	stomach
14	chr3:60595800-60596400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:60595800-60596600	Enhancers	Adipose Nuclei	Adipose
16	chr3:60595800-60596600	Enhancers	Brain Germinal Matrix	brain

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Input of quick search could be:

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

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