Variant report

Variant	rs7734879
Chromosome Location	chr5:60711632-60711633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60704554..60708458-chr5:60711463..60715174,4	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10041978	0.87[ASN][1000 genomes]
rs1045352	0.87[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[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];0.88[AMR][1000 genomes]
rs10939900	1.00[CHB][hapmap];0.96[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	0.90[AMR][1000 genomes]
rs11742658	0.90[AMR][1000 genomes]
rs11743711	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11747564	0.90[AMR][1000 genomes]
rs11749200	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes]
rs11750589	0.98[ASN][1000 genomes]
rs11950318	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11952146	0.82[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[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];0.88[AMR][1000 genomes]
rs11954430	0.81[ASN][1000 genomes]
rs12187112	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13156100	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13157657	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13157831	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13158675	0.99[ASN][1000 genomes]
rs13159018	0.89[AMR][1000 genomes]
rs13159166	0.86[AMR][1000 genomes]
rs13160801	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13162358	0.99[ASN][1000 genomes]
rs13162694	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163970	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13166934	0.88[AMR][1000 genomes]
rs13169711	0.99[ASN][1000 genomes]
rs13170135	0.96[ASN][1000 genomes]
rs13170262	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13171497	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13171757	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13172080	0.93[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];0.86[AMR][1000 genomes]
rs13178686	0.99[ASN][1000 genomes]
rs13179091	0.88[AMR][1000 genomes]
rs13179617	0.85[AMR][1000 genomes]
rs13181015	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13185783	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13186194	0.82[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[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];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13188327	0.92[ASN][1000 genomes]
rs13188685	0.88[AMR][1000 genomes]
rs1348716	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1363892	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1374043	0.81[ASN][1000 genomes]
rs1445979	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445980	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1445981	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1477355	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986252	0.81[ASN][1000 genomes]
rs2034239	0.87[AMR][1000 genomes]
rs2053693	0.89[AMR][1000 genomes]
rs2276987	0.85[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes]
rs28610339	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5027472	0.90[ASN][1000 genomes]
rs55838118	0.93[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];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6449529	0.99[ASN][1000 genomes]
rs6449530	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.98[ASN][1000 genomes]
rs6449531	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449532	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449533	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449535	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6860608	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6865624	0.89[AMR][1000 genomes]
rs6873712	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes]
rs6874264	0.89[AMR][1000 genomes]
rs6874266	0.89[AMR][1000 genomes]
rs6877610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6878927	0.88[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[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];0.89[AMR][1000 genomes]
rs6879809	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6881765	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.99[ASN][1000 genomes]
rs6881799	0.89[AMR][1000 genomes]
rs6882136	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6885005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890351	0.82[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes]
rs6894675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895046	0.81[ASN][1000 genomes]
rs7443602	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7700289	0.99[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7709645	1.00[ASN][1000 genomes]
rs7714457	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714712	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717082	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7719647	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7722810	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7727824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs7734879	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60682600-60712400	Weak transcription	Esophagus	oesophagus
2	chr5:60687600-60711800	Weak transcription	Aorta	Aorta
3	chr5:60698000-60725400	Weak transcription	Spleen	Spleen
4	chr5:60705200-60727200	Weak transcription	Fetal Stomach	stomach
5	chr5:60705400-60713400	Weak transcription	Brain Germinal Matrix	brain
6	chr5:60705400-60713600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:60705600-60712200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:60705600-60719000	Weak transcription	Fetal Brain Male	brain
9	chr5:60706000-60711800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:60706000-60711800	Weak transcription	Fetal Kidney	kidney
11	chr5:60706000-60712200	Weak transcription	Small Intestine	intestine
12	chr5:60706000-60713400	Weak transcription	Adipose Nuclei	Adipose
13	chr5:60706000-60713600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:60706000-60719200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:60706000-60721400	Weak transcription	Fetal Intestine Large	intestine
16	chr5:60706000-60728000	Weak transcription	Fetal Intestine Small	intestine
17	chr5:60706200-60711800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:60706200-60712000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:60706200-60719400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:60706200-60727800	Weak transcription	HUVEC	blood vessel
21	chr5:60707000-60711800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:60707000-60711800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:60707000-60711800	Weak transcription	Osteobl	bone
24	chr5:60707000-60712000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:60707000-60712200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:60707000-60712200	Weak transcription	HSMMtube	muscle
27	chr5:60707000-60712400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:60707200-60711800	Weak transcription	NH-A	brain
29	chr5:60708200-60712000	Weak transcription	HSMM	muscle
30	chr5:60708200-60712200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:60708400-60711800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:60708400-60712000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:60708400-60713400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:60708400-60719200	Weak transcription	Ovary	ovary
35	chr5:60708600-60711800	Weak transcription	Fetal Lung	lung
36	chr5:60708800-60712400	Weak transcription	Fetal Brain Female	brain
37	chr5:60709800-60712000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:60709800-60712600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:60709800-60712800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:60709800-60713200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:60709800-60713800	Enhancers	Brain Substantia Nigra	brain
42	chr5:60709800-60714000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:60709800-60714000	Enhancers	H1 Cell Line	embryonic stem cell
44	chr5:60709800-60714000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr5:60709800-60714000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:60709800-60714000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:60709800-60714000	Enhancers	Brain Anterior Caudate	brain
48	chr5:60709800-60716400	Enhancers	Brain Hippocampus Middle	brain
49	chr5:60710000-60719200	Weak transcription	NHLF	lung
50	chr5:60710200-60711800	Weak transcription	Brain Cingulate Gyrus	brain

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