Variant report

Variant	rs286154
Chromosome Location	chr5:59926911-59926912
allele	A/G
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	chr5:59926595-59929254	K562	blood:	n/a	n/a

Variant related genes	Relation type
DEPDC1B	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10058456	0.80[CHB][hapmap]
rs10805370	1.00[CEU][hapmap]
rs10939857	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10939860	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs10939862	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs11739209	0.87[EUR][1000 genomes]
rs11739724	0.83[EUR][1000 genomes]
rs11740327	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]
rs11741754	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs11745077	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11745627	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747927	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11948543	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11951503	0.83[ASN][1000 genomes]
rs11951950	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11952735	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11955398	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs11956023	0.82[EUR][1000 genomes]
rs11959922	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12514253	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs12515025	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs12517174	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs12517207	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs12522801	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12655515	1.00[CEU][hapmap]
rs1379114	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs1379115	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1379116	0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1379117	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1444237	0.83[JPT][hapmap]
rs1445852	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1456742	0.82[CHB][hapmap]
rs1456743	0.82[CHB][hapmap]
rs1562235	0.83[EUR][1000 genomes]
rs17387940	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs1816899	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867702	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1870014	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs1992612	0.82[CHB][hapmap]
rs2045356	1.00[CEU][hapmap]
rs2061250	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs206789	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs2198865	0.82[ASN][1000 genomes]
rs2409792	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs2591636	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs286148	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs286153	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286155	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs286158	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs2898287	0.84[EUR][1000 genomes]
rs34395679	0.88[EUR][1000 genomes]
rs3857236	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4277863	0.82[CHB][hapmap]
rs4353978	0.86[EUR][1000 genomes]
rs4524466	0.82[CHB][hapmap]
rs4538567	0.90[EUR][1000 genomes]
rs4700378	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4700379	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4700380	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4700381	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55720622	0.84[EUR][1000 genomes]
rs56137970	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56191602	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59155887	0.81[ASN][1000 genomes]
rs62372964	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62373023	0.87[ASN][1000 genomes]
rs62373024	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373025	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449480	0.80[ASN][1000 genomes]
rs6449483	1.00[CEU][hapmap]
rs6449493	0.82[CHB][hapmap]
rs6874072	1.00[CEU][hapmap]
rs755077	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7719726	0.92[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7720233	0.82[CHB][hapmap]
rs7730342	0.82[CHB][hapmap]
rs897672	0.89[CEU][hapmap]
rs9942410	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs286154	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
2	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:59909200-59927000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:59909400-59928800	Weak transcription	HMEC	breast
5	chr5:59920400-59939800	Weak transcription	HSMM	muscle
6	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
7	chr5:59922000-59930200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:59923400-59931800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:59923400-59939800	Weak transcription	K562	blood
10	chr5:59923600-59931200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:59923800-59933400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:59924000-59928800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:59924200-59928200	Weak transcription	GM12878-XiMat	blood
14	chr5:59924200-59929400	Strong transcription	Placenta	Placenta
15	chr5:59924400-59928000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:59924400-59930200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
18	chr5:59924600-59928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:59924600-59930400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:59924600-59936200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:59924800-59927000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:59924800-59929400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:59924800-59929400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:59924800-59930200	Strong transcription	HepG2	liver
25	chr5:59924800-59936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:59925000-59927400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:59925000-59927400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:59925000-59927400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:59925000-59928000	Weak transcription	Lung	lung
30	chr5:59925000-59928800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:59925000-59930000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:59925000-59942800	Strong transcription	Dnd41	blood
33	chr5:59925200-59927000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr5:59925200-59928800	Weak transcription	Fetal Lung	lung
35	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
36	chr5:59925400-59929000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:59925400-59929000	Weak transcription	NHLF	lung
38	chr5:59925800-59928200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:59925800-59928400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr5:59925800-59929600	Strong transcription	Fetal Thymus	thymus
41	chr5:59926000-59929000	Strong transcription	NHEK	skin
42	chr5:59926000-59929400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr5:59926000-59929400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:59926000-59929400	Strong transcription	Fetal Intestine Small	intestine
45	chr5:59926000-59929800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:59926000-59933800	Strong transcription	Fetal Intestine Large	intestine
47	chr5:59926200-59927400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr5:59926200-59927400	ZNF genes & repeats	Primary B cells from cord blood	blood
49	chr5:59926200-59927400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:59926200-59927400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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