Variant report

Variant	rs2061254
Chromosome Location	chr5:59939704-59939705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1026418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs10516154	1.00[ASN][1000 genomes]
rs11957512	1.00[ASN][1000 genomes]
rs11960912	1.00[ASN][1000 genomes]
rs1379111	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16878190	1.00[ASN][1000 genomes]
rs16878304	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878315	1.00[CEU][hapmap]
rs16878426	1.00[CHD][hapmap]
rs16878429	1.00[CHD][hapmap]
rs1870012	1.00[CEU][hapmap]
rs1870013	1.00[CEU][hapmap]
rs2045355	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2061252	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124751	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap]
rs2124753	0.90[AFR][1000 genomes]
rs2409763	1.00[ASN][1000 genomes]
rs2441051	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441052	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591635	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286159	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857237	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887175	1.00[ASN][1000 genomes]
rs3909458	1.00[ASN][1000 genomes]
rs61752571	0.83[AFR][1000 genomes]
rs6872509	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702459	1.00[CEU][hapmap]
rs7706896	1.00[CEU][hapmap]
rs7708849	1.00[CEU][hapmap]
rs7712043	1.00[CEU][hapmap]
rs7719525	1.00[CEU][hapmap]
rs7728865	1.00[ASN][1000 genomes]
rs897671	1.00[CEU][hapmap]
rs9686946	1.00[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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59920400-59939800	Weak transcription	HSMM	muscle
2	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
3	chr5:59923400-59939800	Weak transcription	K562	blood
4	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
5	chr5:59925000-59942800	Strong transcription	Dnd41	blood
6	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
7	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:59927400-59941200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:59928400-59942800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:59929400-59942800	Weak transcription	Fetal Intestine Small	intestine
13	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:59929600-59948000	Weak transcription	NHEK	skin
17	chr5:59930000-59943400	Strong transcription	Placenta	Placenta
18	chr5:59930200-59941200	Weak transcription	Fetal Lung	lung
19	chr5:59931200-59942600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:59931400-59941400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:59932000-59944200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:59932400-59940600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:59932400-59941800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:59932800-59941200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:59933200-59942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:59933600-59940600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:59933600-59944000	Weak transcription	Fetal Stomach	stomach
29	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:59933800-59942400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:59934000-59943000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:59934800-59947600	Weak transcription	HMEC	breast
33	chr5:59936000-59941400	Strong transcription	HepG2	liver
34	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
35	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
36	chr5:59937000-59943000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:59937000-59945800	Weak transcription	GM12878-XiMat	blood
38	chr5:59937400-59941200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:59937400-59943400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:59937600-59940600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:59937600-59941000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr5:59937800-59940600	Strong transcription	Fetal Intestine Large	intestine
43	chr5:59938000-59940600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:59938000-59942600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:59938200-59940600	Strong transcription	A549	lung
46	chr5:59938600-59939800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:59938600-59945200	Weak transcription	Fetal Kidney	kidney
48	chr5:59938800-59939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:59938800-59943000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:59939200-59940000	Strong transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links