Variant report

Variant	rs616113
Chromosome Location	chr3:54664648-54664649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1366032	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496625	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500382	0.95[ASN][1000 genomes]
rs551799	0.84[EUR][1000 genomes]
rs595040	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs595993	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs626074	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs661201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662565	0.82[ASN][1000 genomes]
rs667612	0.84[EUR][1000 genomes]
rs670335	0.85[EUR][1000 genomes]
rs674542	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54660400-54666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:54662400-54665200	Strong transcription	Right Atrium	heart
6	chr3:54663000-54664800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:54663000-54666200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:54663000-54667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:54663200-54665000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:54663200-54667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:54663800-54665000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:54663800-54667400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:54663800-54667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:54664200-54664800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:54664200-54665200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:54664200-54665400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:54664200-54665400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:54664400-54665200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:54664600-54665200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:54664600-54666400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:54664600-54667200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links