Variant report

Variant	rs1038485
Chromosome Location	chr3:154988316-154988317
allele	A/G
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:19)

rs_ID	r²[population]
rs1021215	0.88[AFR][1000 genomes]
rs1117032	0.81[AFR][1000 genomes]
rs13069769	0.89[EUR][1000 genomes]
rs1385483	0.88[AFR][1000 genomes]
rs1531942	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2171016	0.83[AFR][1000 genomes]
rs2171017	0.81[AFR][1000 genomes]
rs2291357	0.81[EUR][1000 genomes]
rs2315039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542981	0.81[AFR][1000 genomes]
rs4555483	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56824726	0.92[EUR][1000 genomes]
rs59587542	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62279087	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6765397	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6809289	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289952	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs984920	0.88[AFR][1000 genomes]
rs9883427	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv829762	chr3:154879350-155052986	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154971600-154996200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:154980800-154988600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:154981200-154995200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:154984600-154988400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:154986400-154988600	Weak transcription	Esophagus	oesophagus
6	chr3:154987400-154996200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:154987800-154988800	Flanking Active TSS	K562	blood
8	chr3:154987800-154989000	Enhancers	HMEC	breast
9	chr3:154987800-154989200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:154987800-154989200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:154987800-154989200	Enhancers	NHEK	skin
12	chr3:154988200-154989400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:154988200-154989600	Enhancers	Placenta	Placenta

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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