Variant report

Variant	rs286158
Chromosome Location	chr5:59934253-59934254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59932997..59935929-chr5:59937074..59939213,2	MCF-7	breast:
2	chr5:59933171..59934818-chr5:59991480..59994360,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10043291	0.85[CHB][hapmap]
rs10058456	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs10939855	0.81[ASN][1000 genomes]
rs10939856	0.82[ASN][1000 genomes]
rs10939860	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs10939862	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs11739724	0.82[ASN][1000 genomes]
rs11740327	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs11741754	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs11948543	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs11951503	0.91[ASN][1000 genomes]
rs11951950	0.85[ASN][1000 genomes]
rs11952735	0.91[ASN][1000 genomes]
rs11955398	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs11956023	0.88[ASN][1000 genomes]
rs11959922	0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs12514253	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12515025	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12517174	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12517207	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12522801	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs1379114	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs1379115	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1379116	0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs1379117	0.91[ASN][1000 genomes]
rs1444237	0.81[JPT][hapmap]
rs1456742	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1456743	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1460958	0.81[JPT][hapmap]
rs1562235	0.85[ASN][1000 genomes]
rs17387940	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs1870014	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs187481	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1992612	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2061250	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs206789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2198865	0.90[ASN][1000 genomes]
rs2409791	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2409792	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs249070	0.84[ASN][1000 genomes]
rs2591636	0.89[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs286154	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs286155	0.94[ASN][1000 genomes]
rs286156	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898287	0.85[ASN][1000 genomes]
rs35382	0.81[JPT][hapmap]
rs35383	0.81[JPT][hapmap]
rs35384	0.81[JPT][hapmap]
rs3857236	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3958943	0.84[ASN][1000 genomes]
rs4277863	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4307050	0.90[CEU][hapmap]
rs4326096	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4515250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4524466	0.95[CHB][hapmap]
rs4699959	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4700378	0.81[ASN][1000 genomes]
rs4700379	0.83[ASN][1000 genomes]
rs4700380	0.89[ASN][1000 genomes]
rs4700381	0.86[ASN][1000 genomes]
rs5012862	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55720622	0.81[ASN][1000 genomes]
rs55768631	0.84[ASN][1000 genomes]
rs56137970	0.85[ASN][1000 genomes]
rs56166952	0.89[ASN][1000 genomes]
rs56191602	0.90[ASN][1000 genomes]
rs59155887	0.89[ASN][1000 genomes]
rs62372964	0.86[ASN][1000 genomes]
rs6449478	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6449480	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6449484	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs6449493	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6877561	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896680	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6896942	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755077	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7720233	0.90[CHB][hapmap]
rs7725028	0.86[AMR][1000 genomes]
rs7730342	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9942410	0.95[CHB][hapmap];0.88[JPT][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs286158	DEPDC1B	cis	cerebellum	SCAN
rs286158	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL
rs286158	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59920400-59939800	Weak transcription	HSMM	muscle
2	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
3	chr5:59923400-59939800	Weak transcription	K562	blood
4	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
5	chr5:59924600-59936200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:59924800-59936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:59925000-59942800	Strong transcription	Dnd41	blood
8	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
9	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:59927400-59935200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:59927400-59941200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:59928400-59942800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:59928600-59935800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:59929400-59934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:59929400-59942800	Weak transcription	Fetal Intestine Small	intestine
18	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:59929600-59935200	Weak transcription	Fetal Thymus	thymus
22	chr5:59929600-59948000	Weak transcription	NHEK	skin
23	chr5:59930000-59943400	Strong transcription	Placenta	Placenta
24	chr5:59930200-59935400	Weak transcription	Thymus	Thymus
25	chr5:59930200-59936400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:59930200-59936400	Weak transcription	GM12878-XiMat	blood
27	chr5:59930200-59939600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:59930200-59941200	Weak transcription	Fetal Lung	lung
29	chr5:59930800-59938800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:59930800-59939200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:59931000-59935800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr5:59931200-59935200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:59931200-59942600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:59931400-59941400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:59931800-59934800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:59932000-59944200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:59932200-59936400	Weak transcription	Fetal Kidney	kidney
38	chr5:59932400-59935000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:59932400-59940600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:59932400-59941800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:59932600-59935200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:59932800-59941200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:59933000-59934800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:59933000-59934800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:59933000-59935800	Strong transcription	HepG2	liver
46	chr5:59933200-59934800	Strong transcription	HMEC	breast
47	chr5:59933200-59942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:59933400-59934800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:59933600-59934800	Strong transcription	Hela-S3	cervix

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