Variant report

Variant	rs11740327
Chromosome Location	chr5:59899413-59899414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10050803	0.88[CEU][hapmap]
rs10058456	0.86[CEU][hapmap];0.80[CHB][hapmap]
rs10805370	0.85[CEU][hapmap]
rs10939860	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs10939862	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11739724	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11741754	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs11745627	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948543	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11951503	0.81[ASN][1000 genomes]
rs11951950	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11952735	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11955398	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs11956023	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11959922	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12186391	0.81[EUR][1000 genomes]
rs12514253	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs12515025	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs12517174	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs12517207	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs12522801	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs12655515	0.85[CEU][hapmap]
rs1379114	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs1379115	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs1379116	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1379117	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1444237	0.83[JPT][hapmap]
rs1445852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1456742	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1456743	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1562235	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17387940	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs1816899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1824120	0.82[EUR][1000 genomes]
rs1867702	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1870014	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs1992612	0.82[CHB][hapmap]
rs2045356	0.85[CEU][hapmap]
rs2061250	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs206789	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2409792	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs248911	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs249070	0.81[ASN][1000 genomes]
rs2591636	0.82[EUR][1000 genomes]
rs286148	0.87[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs286154	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286155	0.84[EUR][1000 genomes]
rs286158	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2898287	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3857236	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3958943	0.85[ASN][1000 genomes]
rs4277863	0.82[CHB][hapmap]
rs4524466	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs4538567	0.84[EUR][1000 genomes]
rs4700379	0.86[EUR][1000 genomes]
rs4700380	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55720622	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55768631	0.85[ASN][1000 genomes]
rs56137970	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56166952	0.83[ASN][1000 genomes]
rs56191602	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62372964	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62373023	0.90[ASN][1000 genomes]
rs62373024	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62373025	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449480	0.84[ASN][1000 genomes]
rs6449483	0.86[CEU][hapmap]
rs6449493	0.82[CHB][hapmap]
rs6874072	0.85[CEU][hapmap]
rs755077	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs7707698	0.82[EUR][1000 genomes]
rs7719726	0.87[TSI][hapmap]
rs7720233	0.82[CHB][hapmap]
rs7730342	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs7736518	0.81[EUR][1000 genomes]
rs897672	0.96[CEU][hapmap]
rs9686489	0.81[EUR][1000 genomes]
rs9942410	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]

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
rs11740327	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:59889000-59900800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:59889200-59900600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:59889200-59900800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:59890400-59901600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
14	chr5:59891200-59909200	Weak transcription	HMEC	breast
15	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:59892000-59912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:59893000-59911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:59894000-59900400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:59894000-59906000	Weak transcription	Osteobl	bone
20	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
21	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
22	chr5:59895800-59899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:59896800-59900200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:59897200-59900200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:59897600-59902200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:59897600-59907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:59898400-59899600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:59898400-59900000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:59898400-59901400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr5:59898400-59902400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:59898600-59899600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:59898600-59899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:59898600-59899600	Strong transcription	K562	blood
34	chr5:59898600-59899800	Strong transcription	HepG2	liver
35	chr5:59898600-59900000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:59898800-59899600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:59898800-59907200	Weak transcription	GM12878-XiMat	blood
38	chr5:59899000-59901800	Strong transcription	Placenta	Placenta
39	chr5:59899000-59905800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:59899200-59910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:59899400-59907200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:59899400-59907600	Weak transcription	Dnd41	blood
43	chr5:59899400-59910800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:59899400-59912600	Weak transcription	Fetal Thymus	thymus
45	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum

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