Variant report

Variant	rs34640
Chromosome Location	chr5:60348715-60348716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10076568	0.81[JPT][hapmap]
rs10471503	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11744226	0.82[ASN][1000 genomes]
rs11951504	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11951606	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13179721	0.91[ASN][1000 genomes]
rs13185516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13357828	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs158565	0.84[EUR][1000 genomes]
rs158566	0.84[EUR][1000 genomes]
rs158567	0.84[EUR][1000 genomes]
rs158568	0.84[EUR][1000 genomes]
rs158569	0.84[EUR][1000 genomes]
rs162229	0.84[EUR][1000 genomes]
rs162231	0.84[EUR][1000 genomes]
rs162232	0.84[EUR][1000 genomes]
rs162233	0.84[EUR][1000 genomes]
rs162235	0.84[EUR][1000 genomes]
rs162236	0.82[EUR][1000 genomes]
rs162237	0.81[EUR][1000 genomes]
rs248678	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs248679	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs248680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs290508	0.80[EUR][1000 genomes]
rs2909851	0.90[EUR][1000 genomes]
rs2950232	0.84[EUR][1000 genomes]
rs295556	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295557	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295565	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs295567	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs329614	0.82[EUR][1000 genomes]
rs329615	0.81[EUR][1000 genomes]
rs329618	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34425764	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34595	0.90[EUR][1000 genomes]
rs34598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34599	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34641	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35383830	0.83[ASN][1000 genomes]
rs6449509	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6871236	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs767634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9291704	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9291707	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34640	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60324600-60354000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
3	chr5:60344800-60353400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:60345600-60350800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:60345800-60349600	Enhancers	Fetal Intestine Large	intestine
6	chr5:60345800-60349600	Enhancers	Fetal Intestine Small	intestine
7	chr5:60346200-60349200	Enhancers	NH-A	brain
8	chr5:60346200-60349400	Enhancers	HSMM	muscle
9	chr5:60346200-60349600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:60346200-60350400	Enhancers	NHDF-Ad	bronchial
11	chr5:60346400-60350000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:60346400-60350200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:60346400-60350400	Enhancers	HMEC	breast
14	chr5:60346400-60350400	Enhancers	Osteobl	bone
15	chr5:60346600-60350400	Enhancers	NHEK	skin
16	chr5:60346800-60349600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:60346800-60350400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:60346800-60350600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:60347000-60349000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:60347000-60350000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:60347000-60350600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:60347200-60349600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:60347200-60379200	Weak transcription	Ovary	ovary
24	chr5:60347400-60348800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:60347400-60349800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:60347400-60351400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:60347400-60353000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:60347400-60356000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:60347600-60349000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:60347800-60348800	Weak transcription	HUVEC	blood vessel
31	chr5:60347800-60353000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:60348000-60349000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:60348400-60348800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:60348400-60348800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:60348400-60349600	Enhancers	Hela-S3	cervix
36	chr5:60348600-60348800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr5:60348600-60349000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:60348600-60349200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr5:60348600-60349400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:60348600-60349400	Flanking Active TSS	A549	lung
41	chr5:60348600-60349600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr5:60348600-60350400	Enhancers	NHLF	lung

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