Variant report

Variant	rs3857236
Chromosome Location	chr5:59909529-59909530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10043291	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10050803	0.88[CEU][hapmap]
rs10058456	0.86[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs10805370	0.85[CEU][hapmap]
rs10939855	0.84[ASN][1000 genomes]
rs10939856	0.85[ASN][1000 genomes]
rs10939860	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs10939862	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs11739724	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11740327	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]
rs11741754	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11745627	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11948543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951503	0.97[ASN][1000 genomes]
rs11951950	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11952735	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955398	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11956023	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11959922	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]
rs12186391	0.82[EUR][1000 genomes]
rs12514253	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs12515025	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs12517174	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12517207	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12522801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs12655515	0.85[CEU][hapmap]
rs1379114	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs1379115	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs1379116	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1379117	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444237	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1445852	0.84[EUR][1000 genomes]
rs1456742	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1456743	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1460958	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1562235	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17387940	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1816899	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1824120	0.83[EUR][1000 genomes]
rs1867702	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1870014	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs1992612	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2045356	0.85[CEU][hapmap]
rs2061250	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs206789	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2198865	0.94[ASN][1000 genomes]
rs2409792	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs248911	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs249070	0.90[ASN][1000 genomes]
rs2591636	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs286154	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]
rs286155	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs286156	0.89[ASN][1000 genomes]
rs286158	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2898287	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3958943	0.94[ASN][1000 genomes]
rs4277863	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4524466	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4538567	0.86[EUR][1000 genomes]
rs4699959	0.83[ASN][1000 genomes]
rs4700378	0.87[ASN][1000 genomes]
rs4700379	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700380	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700381	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5012862	0.87[ASN][1000 genomes]
rs55720622	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55768631	0.94[ASN][1000 genomes]
rs56137970	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56166952	1.00[ASN][1000 genomes]
rs56191602	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59155887	0.92[ASN][1000 genomes]
rs62372964	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373024	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62373025	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6449483	0.86[CEU][hapmap]
rs6449493	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6874072	0.85[CEU][hapmap]
rs6877561	0.89[ASN][1000 genomes]
rs6896942	0.85[ASN][1000 genomes]
rs755077	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs7707698	0.83[EUR][1000 genomes]
rs7719726	0.87[TSI][hapmap]
rs7720233	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7730342	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7736518	0.82[EUR][1000 genomes]
rs897672	0.96[CEU][hapmap]
rs9686489	0.82[EUR][1000 genomes]
rs9942410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]

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	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
rs3857236	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:59892000-59912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:59893000-59911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
11	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
12	chr5:59899200-59910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:59899400-59910800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:59899400-59912600	Weak transcription	Fetal Thymus	thymus
15	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:59899600-59910000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:59899800-59924800	Weak transcription	HepG2	liver
18	chr5:59900000-59910600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:59901800-59911400	Weak transcription	Placenta	Placenta
20	chr5:59902200-59924800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:59908400-59910000	Strong transcription	Dnd41	blood
22	chr5:59908600-59910000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:59908600-59910000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:59909000-59910000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:59909000-59910000	Enhancers	NHEK	skin
26	chr5:59909200-59927000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:59909400-59909800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:59909400-59911000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:59909400-59911000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:59909400-59928800	Weak transcription	HMEC	breast

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