Variant report

Variant	rs1445852
Chromosome Location	chr5:59891304-59891305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10805370	1.00[CEU][hapmap]
rs10939857	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10939860	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs10939862	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs11739209	0.84[EUR][1000 genomes]
rs11739724	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11740327	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11745077	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11745627	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747927	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11948543	0.85[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11951950	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952735	0.82[EUR][1000 genomes]
rs11959922	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs12514253	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs12515025	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs12522801	0.88[CEU][hapmap]
rs12655515	1.00[CEU][hapmap]
rs1379114	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs1379115	0.85[CEU][hapmap]
rs1379116	0.92[JPT][hapmap]
rs1379117	0.82[EUR][1000 genomes]
rs1562235	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1816899	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867702	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1870014	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs2045356	1.00[CEU][hapmap]
rs2061250	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs206789	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs2409792	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs2591636	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs286148	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs286153	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs286154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286155	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs286158	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs2898287	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34395679	0.85[EUR][1000 genomes]
rs3857236	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4353978	0.84[EUR][1000 genomes]
rs4538567	0.87[EUR][1000 genomes]
rs4700378	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4700379	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4700380	0.83[EUR][1000 genomes]
rs4700381	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55720622	0.82[EUR][1000 genomes]
rs56137970	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62372964	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62373023	0.81[ASN][1000 genomes]
rs62373024	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62373025	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6449480	0.94[ASN][1000 genomes]
rs6449483	1.00[CEU][hapmap]
rs6874072	1.00[CEU][hapmap]
rs755077	0.85[CEU][hapmap]
rs7719726	0.92[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs897672	0.89[CEU][hapmap]
rs9942410	0.85[CEU][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	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1445852	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
6	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:59883400-59893600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:59883400-59894200	Weak transcription	Placenta	Placenta
10	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:59885000-59895800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:59885200-59895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:59885400-59894400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:59886600-59894400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:59888800-59893400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:59889000-59891400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:59889000-59900800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:59889200-59891400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr5:59889200-59900600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:59889200-59900800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:59889400-59893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:59889600-59893600	Weak transcription	Thymus	Thymus
25	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
26	chr5:59890400-59901600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:59890600-59891600	Strong transcription	Dnd41	blood
28	chr5:59890800-59891400	Enhancers	Fetal Lung	lung
29	chr5:59890800-59892200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:59890800-59897600	Strong transcription	HepG2	liver
31	chr5:59891000-59893400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:59891200-59891600	Enhancers	Primary T cells from cord blood	blood
34	chr5:59891200-59892400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:59891200-59894200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:59891200-59896400	Weak transcription	HUVEC	blood vessel
37	chr5:59891200-59909200	Weak transcription	HMEC	breast
38	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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