Variant report

Variant	rs17669257
Chromosome Location	chr3:60566161-60566162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13076604	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs180987	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs180992	0.88[CHB][hapmap];0.87[YRI][hapmap]
rs180993	0.88[CHB][hapmap]
rs180998	0.84[ASW][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap]
rs2594233	0.84[AFR][1000 genomes]
rs56101492	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6807877	0.83[LWK][hapmap]
rs7634073	0.83[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs9845479	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17669257	FAM107A	cis	parietal	SCAN
rs17669257	ARF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60555400-60573600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:60561800-60566400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:60561800-60567800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:60561800-60573400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:60562000-60567600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:60562200-60566600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:60562400-60566400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:60562400-60568600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:60565000-60570800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:60565200-60566200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:60565400-60566600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:60565800-60567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:60566000-60566400	Weak transcription	Aorta	Aorta
14	chr3:60566000-60569600	Weak transcription	Osteobl	bone
15	chr3:60566000-60569800	Weak transcription	NH-A	brain
16	chr3:60566000-60573800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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