Variant report

Variant	rs6449533
Chromosome Location	chr5:60722644-60722645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10041978	0.87[ASN][1000 genomes]
rs1045352	0.94[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs10939900	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.99[ASN][1000 genomes]
rs10939901	0.99[ASN][1000 genomes]
rs10939902	1.00[ASN][1000 genomes]
rs10939903	0.87[ASN][1000 genomes]
rs10939905	0.85[AMR][1000 genomes]
rs11742658	0.85[AMR][1000 genomes]
rs11743711	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11747564	0.89[AMR][1000 genomes]
rs11749200	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs11750589	0.98[ASN][1000 genomes]
rs11950318	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11952146	0.88[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs11954430	0.81[ASN][1000 genomes]
rs12187112	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188627	0.94[ASN][1000 genomes]
rs12189001	0.99[ASN][1000 genomes]
rs12518479	0.99[ASN][1000 genomes]
rs12520628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12522647	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13156100	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13157657	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13157831	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13158675	0.99[ASN][1000 genomes]
rs13159018	0.84[AMR][1000 genomes]
rs13159166	0.80[AMR][1000 genomes]
rs13160801	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13162358	0.99[ASN][1000 genomes]
rs13162694	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163970	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13166934	0.82[AMR][1000 genomes]
rs13169711	0.99[ASN][1000 genomes]
rs13170135	0.96[ASN][1000 genomes]
rs13170262	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13171497	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13171757	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172080	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13172084	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs13178686	0.99[ASN][1000 genomes]
rs13179091	0.82[AMR][1000 genomes]
rs13181015	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13185783	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13186194	0.88[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13188327	0.92[ASN][1000 genomes]
rs13188685	0.82[AMR][1000 genomes]
rs1348716	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1363892	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1374043	0.81[ASN][1000 genomes]
rs1445979	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445980	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1445981	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1477355	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986252	0.81[ASN][1000 genomes]
rs2034239	0.81[AMR][1000 genomes]
rs2053693	0.84[AMR][1000 genomes]
rs2276987	0.85[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs28610339	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739794	0.96[ASN][1000 genomes]
rs35262187	0.99[ASN][1000 genomes]
rs4276369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4392578	0.99[ASN][1000 genomes]
rs4484384	0.99[ASN][1000 genomes]
rs4604142	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5027472	0.90[ASN][1000 genomes]
rs55838118	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56035042	0.99[ASN][1000 genomes]
rs60529601	0.99[ASN][1000 genomes]
rs60886975	0.99[ASN][1000 genomes]
rs62368660	0.99[ASN][1000 genomes]
rs6449528	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6449529	0.99[ASN][1000 genomes]
rs6449530	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.98[ASN][1000 genomes]
rs6449531	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449532	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449535	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6860608	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6865624	0.84[AMR][1000 genomes]
rs6873712	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs6874264	0.84[AMR][1000 genomes]
rs6874266	0.84[AMR][1000 genomes]
rs6877610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6878927	0.94[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs6879809	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6881765	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.99[ASN][1000 genomes]
rs6881799	0.83[AMR][1000 genomes]
rs6882136	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6885005	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890351	0.88[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6894675	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895046	0.81[ASN][1000 genomes]
rs7443602	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7700289	0.99[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7709645	1.00[ASN][1000 genomes]
rs7714457	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714712	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717082	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7719647	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7722810	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7727824	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734879	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6449533	DEPDC1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60698000-60725400	Weak transcription	Spleen	Spleen
2	chr5:60705200-60727200	Weak transcription	Fetal Stomach	stomach
3	chr5:60706000-60728000	Weak transcription	Fetal Intestine Small	intestine
4	chr5:60706200-60727800	Weak transcription	HUVEC	blood vessel
5	chr5:60711000-60735800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:60712600-60727600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:60712800-60725400	Weak transcription	Pancreas	Pancrea
8	chr5:60713400-60732800	Weak transcription	Small Intestine	intestine
9	chr5:60713800-60724400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:60714000-60725000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:60714000-60725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:60714000-60725600	Weak transcription	Stomach Mucosa	stomach
13	chr5:60714000-60727800	Weak transcription	Brain Germinal Matrix	brain
14	chr5:60717200-60726200	Weak transcription	Primary B cells from cord blood	blood
15	chr5:60717400-60724800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:60719200-60723600	Enhancers	Brain Angular Gyrus	brain
17	chr5:60719200-60729400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:60719600-60726600	Weak transcription	Thymus	Thymus
19	chr5:60719800-60724600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:60719800-60724600	Weak transcription	Liver	Liver
21	chr5:60719800-60725400	Weak transcription	Fetal Kidney	kidney
22	chr5:60719800-60745200	Weak transcription	NHDF-Ad	bronchial
23	chr5:60720000-60724200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:60720000-60724600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:60720000-60725000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:60720000-60725000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:60720000-60725000	Weak transcription	Gastric	stomach
28	chr5:60720000-60725200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:60720000-60725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:60720000-60725400	Weak transcription	Right Atrium	heart
31	chr5:60720000-60727800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:60720000-60733800	Weak transcription	NHLF	lung
33	chr5:60720000-60736400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:60720000-60737400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:60720200-60724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:60720200-60725200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:60720400-60725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:60720400-60725200	Weak transcription	Fetal Brain Female	brain
39	chr5:60720400-60725200	Weak transcription	Fetal Lung	lung
40	chr5:60720400-60725400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:60720400-60728200	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:60720400-60734000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:60720600-60743200	Weak transcription	HSMMtube	muscle
44	chr5:60720800-60725200	Weak transcription	Left Ventricle	heart
45	chr5:60721000-60722800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:60721000-60733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:60721200-60724200	Weak transcription	Fetal Brain Male	brain
48	chr5:60721400-60722800	Enhancers	Brain Substantia Nigra	brain
49	chr5:60721400-60725600	Weak transcription	Hela-S3	cervix
50	chr5:60721400-60727800	Weak transcription	Stomach Smooth Muscle	stomach

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