Variant report

Variant	rs13100029
Chromosome Location	chr3:54792756-54792757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10510773	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12488046	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490327	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs12490953	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12496821	0.89[CHB][hapmap]
rs13068008	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13070126	0.89[CEU][hapmap];0.81[ASN][1000 genomes]
rs13070262	0.82[ASN][1000 genomes]
rs13083683	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs13084602	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13086256	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13088416	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13090131	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13092066	0.88[ASN][1000 genomes]
rs13095178	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1344671	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520575	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17815840	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1882320	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1882322	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1921548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2099019	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3852006	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs3864001	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3868872	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs3906509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4025824	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4083342	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6808464	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6809269	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809715	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618235	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7618991	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7623961	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7636321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54784600-54797200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:54785200-54793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:54785800-54798200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:54787400-54792800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:54787400-54800200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54787600-54804600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:54789400-54793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:54790000-54794400	Enhancers	Fetal Stomach	stomach
9	chr3:54790600-54794600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:54790800-54793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:54790800-54794200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:54791400-54794000	Weak transcription	NH-A	brain
13	chr3:54791400-54794000	Weak transcription	NHDF-Ad	bronchial
14	chr3:54791800-54794200	Weak transcription	NHLF	lung
15	chr3:54792600-54792800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:54792600-54792800	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:54792600-54793200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links