Variant report

Variant	rs2406914
Chromosome Location	chr5:52920231-52920232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12513928	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12514182	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12515547	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12516733	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518536	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12519736	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12522533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12523552	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1388111	1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs17305186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994648	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2045391	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2054970	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2087619	0.94[YRI][hapmap]
rs56743978	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58919751	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72750157	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750158	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72751823	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72751826	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72751862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751865	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751870	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72753665	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72753667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72753681	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753683	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753687	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753690	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv4828	chr5:52895470-52940279	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2406914	CDC20B	cis	parietal	SCAN
rs2406914	NDUFS4	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52889800-52920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:52899400-52928400	Weak transcription	Fetal Heart	heart
3	chr5:52900800-52936600	Weak transcription	NHEK	skin
4	chr5:52901000-52932600	Weak transcription	Aorta	Aorta
5	chr5:52901400-52920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:52901800-52927000	Weak transcription	Pancreas	Pancrea
7	chr5:52902600-52920800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:52902600-52927000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:52902800-52920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:52902800-52926400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:52903000-52927000	Weak transcription	Left Ventricle	heart
12	chr5:52903000-52943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:52903200-52920800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:52903200-52926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:52903200-52939200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:52903600-52926800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:52904200-52936800	Weak transcription	NHDF-Ad	bronchial
18	chr5:52904400-52920400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:52904400-52966600	Weak transcription	Osteobl	bone
20	chr5:52904600-52937000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:52905000-52920600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:52905000-52928800	Weak transcription	HSMM	muscle
23	chr5:52906400-52926800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:52909200-52920800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:52909200-52927000	Weak transcription	Ovary	ovary
26	chr5:52909600-52937600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:52910600-52920600	Weak transcription	Brain Germinal Matrix	brain
28	chr5:52910600-52941000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:52917800-52921200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:52917800-52922000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:52918000-52920400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr5:52918000-52921200	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr5:52918000-52921200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr5:52918200-52920800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:52918200-52921200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:52918600-52920800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:52919000-52920600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:52919000-52921600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
39	chr5:52919000-52922000	ZNF genes & repeats	Fetal Lung	lung
40	chr5:52919200-52944000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:52919600-52920400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:52919600-52920600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:52919600-52921200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr5:52919600-52921200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr5:52919800-52920800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:52919800-52920800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:52919800-52921000	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr5:52920000-52920600	Weak transcription	Psoas Muscle	Psoas
49	chr5:52920000-52920800	ZNF genes & repeats	HepG2	liver
50	chr5:52920000-52921000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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