Variant report

Variant	rs1563516
Chromosome Location	chr5:59944300-59944301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1026418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1107232	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1107233	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12658660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs1379113	0.83[ASN][1000 genomes]
rs1460959	0.93[CHB][hapmap]
rs1563517	0.93[CHB][hapmap]
rs1563518	0.91[CHB][hapmap]
rs1563519	0.93[CHB][hapmap]
rs1563905	0.93[CHB][hapmap]
rs1563906	0.91[CHB][hapmap]
rs1563907	0.93[CHB][hapmap]
rs16878304	1.00[CEU][hapmap]
rs16878315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1870012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1870013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1992613	0.93[CHB][hapmap]
rs2045355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2061254	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2124751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs2124753	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169254	0.93[CHB][hapmap]
rs2305680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2441052	0.93[AFR][1000 genomes]
rs2591635	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2606688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs286150	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs286151	0.90[AFR][1000 genomes]
rs286152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs286157	1.00[CEU][hapmap]
rs2898298	0.93[CHB][hapmap]
rs34414908	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34915115	0.83[ASN][1000 genomes]
rs3857238	0.93[CHB][hapmap]
rs4273559	0.93[CHB][hapmap]
rs61752571	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6871928	0.93[CHB][hapmap]
rs6872509	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7702459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7706896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7708849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7712043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7713673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7716051	0.93[CHB][hapmap]
rs7719525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7733069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs897671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs897673	0.81[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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
2	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
3	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:59929600-59948000	Weak transcription	NHEK	skin
9	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:59934800-59947600	Weak transcription	HMEC	breast
12	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
13	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
14	chr5:59937000-59945800	Weak transcription	GM12878-XiMat	blood
15	chr5:59938600-59945200	Weak transcription	Fetal Kidney	kidney
16	chr5:59940400-59947800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:59940400-59947800	Weak transcription	HSMM	muscle
18	chr5:59940600-59945000	Weak transcription	Fetal Intestine Large	intestine
19	chr5:59940600-59947400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:59940600-59947600	Weak transcription	A549	lung
21	chr5:59940600-59948000	Weak transcription	K562	blood
22	chr5:59940600-59950200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:59941000-59947200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:59941200-59946600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:59941200-59947600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:59942200-59945400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:59942400-59944400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:59942600-59944800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:59942600-59947400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:59942800-59952000	Weak transcription	Dnd41	blood
31	chr5:59942800-59961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:59943400-59944600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:59943400-59947600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:59943400-59947800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:59943400-59952400	Weak transcription	Placenta	Placenta
36	chr5:59943400-59977000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:59943600-59945000	Enhancers	HepG2	liver
38	chr5:59943800-59945400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:59943800-59952600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:59944000-59944400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr5:59944200-59944400	Enhancers	Primary hematopoietic stem cells	blood

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