Variant report

Variant	rs4326096
Chromosome Location	chr5:59890278-59890279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16878397	1.00[LWK][hapmap]
rs187481	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs206789	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2409791	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs286153	0.85[MEX][hapmap]
rs286154	0.85[MEX][hapmap]
rs286156	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs286158	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4307050	0.85[CEU][hapmap]
rs4515250	0.86[ASW][hapmap];0.95[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4524466	0.81[CHB][hapmap]
rs4699956	1.00[LWK][hapmap]
rs4699959	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5012862	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6449478	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449480	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6449484	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs6877561	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6896680	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs6896942	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7725028	0.87[AMR][1000 genomes]
rs9942410	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4326096	DEPDC1B	cis	cerebellum	SCAN
rs4326096	ZSWIM6	cis	lymphoblastoid	seeQTL
rs4326096	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL
rs4326096	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
7	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:59876400-59890600	Weak transcription	Dnd41	blood
10	chr5:59882200-59890400	Weak transcription	Fetal Intestine Large	intestine
11	chr5:59882200-59890400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:59882200-59890800	Weak transcription	HepG2	liver
13	chr5:59883400-59893600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:59883400-59894200	Weak transcription	Placenta	Placenta
15	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:59885000-59895800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:59885200-59895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:59885400-59894400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:59886600-59894400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:59888800-59893400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:59889000-59890800	Weak transcription	Fetal Lung	lung
23	chr5:59889000-59891400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:59889000-59900800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:59889200-59891200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:59889200-59891400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr5:59889200-59900600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:59889200-59900800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:59889400-59893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:59889600-59891200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr5:59889600-59893600	Weak transcription	Thymus	Thymus
33	chr5:59890200-59890400	ZNF genes & repeats	Fetal Heart	heart
34	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine

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