Variant report

Variant	rs286155
Chromosome Location	chr5:59924909-59924910
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:59923838-59926299	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251303	TF binding region
DEPDC1B	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10043291	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10058456	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs10805370	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs10939855	0.87[ASN][1000 genomes]
rs10939856	0.88[ASN][1000 genomes]
rs10939857	0.87[EUR][1000 genomes]
rs10939860	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10939862	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11739209	0.87[EUR][1000 genomes]
rs11739724	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740327	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs11741754	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11745077	0.88[EUR][1000 genomes]
rs11745627	0.84[EUR][1000 genomes]
rs11747927	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11948543	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951503	0.97[ASN][1000 genomes]
rs11951950	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11952735	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11955398	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11956023	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11959922	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12514253	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12515025	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12517174	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12517207	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12522801	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12655515	1.00[CEU][hapmap];0.97[YRI][hapmap]
rs1379114	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1379115	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1379116	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1379117	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444237	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1445852	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456742	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1456743	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1460958	0.94[JPT][hapmap]
rs1562235	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17387940	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1816899	0.84[EUR][1000 genomes]
rs1867702	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870014	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1992612	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2045356	1.00[CEU][hapmap]
rs2061250	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206789	0.81[CHB][hapmap]
rs2198865	0.96[ASN][1000 genomes]
rs2409792	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs249070	0.87[ASN][1000 genomes]
rs2591636	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs286148	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs286153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286154	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286156	0.94[ASN][1000 genomes]
rs286158	0.95[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2898287	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34395679	0.88[EUR][1000 genomes]
rs3857236	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3958943	0.89[ASN][1000 genomes]
rs4277863	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4353978	0.86[EUR][1000 genomes]
rs4524466	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4538567	0.90[EUR][1000 genomes]
rs4699959	0.82[ASN][1000 genomes]
rs4700378	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4700379	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700380	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700381	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5012862	0.86[ASN][1000 genomes]
rs55720622	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55768631	0.89[ASN][1000 genomes]
rs56137970	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56166952	0.94[ASN][1000 genomes]
rs56191602	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59155887	0.95[ASN][1000 genomes]
rs62372964	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62373024	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62373025	0.84[EUR][1000 genomes]
rs6449483	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6449493	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6874072	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6877561	0.94[ASN][1000 genomes]
rs6896942	0.84[ASN][1000 genomes]
rs755077	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7719726	0.92[CEU][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7720233	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs897672	0.89[CEU][hapmap];0.97[YRI][hapmap]
rs9942410	0.86[CEU][hapmap];0.95[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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
4	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
5	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:59909200-59927000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:59909400-59928800	Weak transcription	HMEC	breast
8	chr5:59910000-59925000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:59910000-59925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:59911800-59926000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:59911800-59926000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:59911800-59926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:59915800-59926200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:59920400-59939800	Weak transcription	HSMM	muscle
15	chr5:59920600-59925000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
17	chr5:59921600-59925000	Weak transcription	Dnd41	blood
18	chr5:59921600-59925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:59921600-59926400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:59922000-59930200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:59922200-59926200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:59922600-59926800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:59922800-59925000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:59922800-59926200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:59922800-59926200	Weak transcription	Fetal Stomach	stomach
26	chr5:59923400-59926000	Weak transcription	Fetal Intestine Small	intestine
27	chr5:59923400-59926200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:59923400-59931800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:59923400-59939800	Weak transcription	K562	blood
30	chr5:59923600-59931200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:59923800-59933400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:59924000-59926000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:59924000-59928800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:59924200-59926000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:59924200-59926000	Weak transcription	NHEK	skin
36	chr5:59924200-59926200	Weak transcription	Aorta	Aorta
37	chr5:59924200-59928200	Weak transcription	GM12878-XiMat	blood
38	chr5:59924200-59929400	Strong transcription	Placenta	Placenta
39	chr5:59924400-59926800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:59924400-59928000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:59924400-59930200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
43	chr5:59924600-59925000	Strong transcription	Fetal Thymus	thymus
44	chr5:59924600-59928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:59924600-59930400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:59924600-59936200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:59924800-59925000	Active TSS	Lung	lung
48	chr5:59924800-59925200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr5:59924800-59925200	Strong transcription	Fetal Intestine Large	intestine
50	chr5:59924800-59926200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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