Variant report

Variant	rs11959922
Chromosome Location	chr5:59920607-59920608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10043291	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs10050803	0.89[CEU][hapmap]
rs10058456	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10805370	0.86[CEU][hapmap]
rs10939855	0.88[ASN][1000 genomes]
rs10939856	0.89[ASN][1000 genomes]
rs10939860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs10939862	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs11739724	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740327	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]
rs11741754	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11745627	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11948543	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11951503	0.99[ASN][1000 genomes]
rs11951950	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11952735	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11955398	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11956023	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12186391	0.83[EUR][1000 genomes]
rs12514253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs12515025	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs12517174	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12517207	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12522801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs12655515	0.85[CEU][hapmap]
rs1379114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs1379115	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs1379116	0.95[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs1379117	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1444237	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs1445852	0.83[EUR][1000 genomes]
rs1456742	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1456743	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1460958	0.86[JPT][hapmap]
rs1562235	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17387940	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1816899	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1824120	0.84[EUR][1000 genomes]
rs1867702	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1870014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs1992612	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2045356	0.86[CEU][hapmap]
rs2061250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs206789	0.81[CHB][hapmap]
rs2198865	0.98[ASN][1000 genomes]
rs2409792	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs248911	0.88[EUR][1000 genomes]
rs249070	0.89[ASN][1000 genomes]
rs2591636	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs286154	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs286155	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs286156	0.92[ASN][1000 genomes]
rs286158	0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs2898287	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3857236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3958943	0.90[ASN][1000 genomes]
rs4277863	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4524466	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs4538567	0.87[EUR][1000 genomes]
rs4699959	0.80[ASN][1000 genomes]
rs4700378	0.83[ASN][1000 genomes]
rs4700379	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4700380	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700381	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5012862	0.84[ASN][1000 genomes]
rs55720622	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55768631	0.90[ASN][1000 genomes]
rs56137970	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56166952	0.96[ASN][1000 genomes]
rs56191602	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59155887	0.96[ASN][1000 genomes]
rs62372964	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62373024	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62373025	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6449483	0.87[CEU][hapmap]
rs6449493	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6874072	0.86[CEU][hapmap]
rs6877561	0.92[ASN][1000 genomes]
rs6896942	0.82[ASN][1000 genomes]
rs755077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs7707698	0.84[EUR][1000 genomes]
rs7720233	0.95[CHB][hapmap]
rs7730342	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs7736518	0.83[EUR][1000 genomes]
rs897672	0.96[CEU][hapmap]
rs9686489	0.83[EUR][1000 genomes]
rs9942410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[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	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
rs11959922	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
4	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
5	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:59899800-59924800	Weak transcription	HepG2	liver
7	chr5:59902200-59924800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:59909200-59927000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:59909400-59928800	Weak transcription	HMEC	breast
10	chr5:59910000-59921200	Weak transcription	Dnd41	blood
11	chr5:59910000-59925000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:59910000-59925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:59911800-59923600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:59911800-59924200	Weak transcription	Placenta	Placenta
15	chr5:59911800-59926000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:59911800-59926000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:59911800-59926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:59912000-59924600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:59915800-59926200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:59916200-59924800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:59917800-59924600	Weak transcription	Fetal Thymus	thymus
22	chr5:59918600-59924800	Weak transcription	Fetal Intestine Large	intestine
23	chr5:59919000-59922000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:59919800-59924800	Weak transcription	A549	lung
25	chr5:59920200-59921200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:59920400-59939800	Weak transcription	HSMM	muscle
27	chr5:59920600-59921400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:59920600-59925000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel

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