Variant report

Variant	rs6042313
Chromosome Location	chr20:13691562-13691563
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10485767	0.89[CHB][hapmap]
rs12625600	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2297050	0.89[YRI][hapmap]
rs3789336	0.89[CHB][hapmap]
rs4813138	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4813143	0.89[CHB][hapmap]
rs4814253	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6042333	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6105160	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6105163	0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs6110019	0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs6110023	0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs6110037	0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs6110050	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6514441	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7360405	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs736365	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv1793063	chr20:13691562-13708788	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6042313	ESF1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13689000-13694400	Weak transcription	Primary B cells from cord blood	blood
2	chr20:13690000-13694000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr20:13690200-13696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr20:13690400-13691800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:13690400-13692800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr20:13690400-13697000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:13690600-13691600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr20:13690600-13694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:13690600-13694000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr20:13690600-13695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
12	chr20:13690800-13691800	Weak transcription	Primary T cells from cord blood	blood
13	chr20:13691000-13691600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr20:13691000-13692600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr20:13691000-13692800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:13691000-13692800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr20:13691000-13693800	Weak transcription	Left Ventricle	heart
18	chr20:13691200-13692400	ZNF genes & repeats	Dnd41	blood
19	chr20:13691200-13692800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr20:13691200-13695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:13691400-13692600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:13691400-13693600	Weak transcription	Fetal Intestine Large	intestine
23	chr20:13691400-13694000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr20:13691400-13694200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr20:13691400-13694200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:13691400-13694200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr20:13691400-13694200	Weak transcription	Osteobl	bone
28	chr20:13691400-13696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:13691400-13696200	Weak transcription	Right Ventricle	heart

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