Variant report

Variant	rs2553448
Chromosome Location	chr4:106697812-106697813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10017111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10023798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10032269	1.00[JPT][hapmap]
rs10516520	1.00[JPT][hapmap]
rs10516521	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10516524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11097896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721732	1.00[JPT][hapmap]
rs11721842	1.00[JPT][hapmap]
rs11730825	1.00[JPT][hapmap]
rs1294668	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1294671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1294672	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1447097	1.00[JPT][hapmap]
rs17035915	1.00[JPT][hapmap]
rs17035936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17035939	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17035951	1.00[JPT][hapmap]
rs17259503	1.00[JPT][hapmap]
rs17259931	1.00[JPT][hapmap]
rs17260120	1.00[JPT][hapmap]
rs17260183	1.00[JPT][hapmap]
rs17260856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17261786	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17262443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17262457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17263714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17264527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17325276	1.00[JPT][hapmap]
rs1862081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2098571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2112047	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2112049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2161046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2193855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2193856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2193857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2216515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2216516	0.95[ASN][1000 genomes]
rs2256746	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305212	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544399	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544401	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544414	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544417	0.82[CHB][hapmap];0.95[ASN][1000 genomes]
rs2544418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553452	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2553464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553469	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2866781	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796923	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3943980	0.95[ASN][1000 genomes]
rs4324546	1.00[JPT][hapmap]
rs4324547	1.00[JPT][hapmap]
rs4326019	1.00[JPT][hapmap]
rs4407508	1.00[JPT][hapmap]
rs4588463	1.00[JPT][hapmap]
rs56843185	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73837092	0.81[EUR][1000 genomes]
rs73837096	0.81[EUR][1000 genomes]
rs73839004	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73839006	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73839007	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73839008	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73839010	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7666969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7676226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7681991	1.00[JPT][hapmap]
rs7687176	1.00[JPT][hapmap]
rs7698817	1.00[JPT][hapmap]
rs961472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs961473	1.00[CHB][hapmap];1.00[JPT][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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv879700	chr4:106643445-106745057	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000947	chr4:106651153-106701679	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106685400-106700000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:106687000-106698400	Weak transcription	Fetal Lung	lung
3	chr4:106687800-106699600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:106688400-106708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:106689000-106698800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:106689200-106703600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:106689400-106706000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:106690800-106706000	Weak transcription	Fetal Heart	heart
9	chr4:106691400-106706400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:106692400-106729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:106694000-106718200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:106694600-106704200	Weak transcription	HepG2	liver
13	chr4:106695000-106698800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:106695200-106757000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:106695600-106703000	Weak transcription	Thymus	Thymus
16	chr4:106696600-106698000	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:106696800-106698000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:106696800-106698000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:106696800-106698000	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr4:106696800-106698000	Strong transcription	Fetal Stomach	stomach
21	chr4:106697200-106725800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:106697400-106698200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:106697800-106704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:106697800-106723200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links