Variant report

Variant	rs6827519
Chromosome Location	chr4:74466409-74466410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11736697	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247583	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs13131954	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142786	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1534642	0.88[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17805665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957660	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2010987	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446944	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6827519	CNOT6L	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74440200-74472600	Weak transcription	Gastric	stomach
2	chr4:74449000-74470200	Weak transcription	Primary T cells from cord blood	blood
3	chr4:74456400-74472200	Weak transcription	Colonic Mucosa	Colon
4	chr4:74463600-74470400	Enhancers	Fetal Intestine Large	intestine
5	chr4:74463800-74474200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:74464200-74476400	Enhancers	Stomach Mucosa	stomach
7	chr4:74464200-74477200	Enhancers	Fetal Intestine Small	intestine
8	chr4:74464600-74467000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:74464800-74466600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
10	chr4:74464800-74467800	Enhancers	Colon Smooth Muscle	Colon
11	chr4:74465000-74475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:74465200-74468800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:74465200-74469000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:74465400-74468400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:74465400-74468800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:74465400-74468800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:74465400-74469000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:74465400-74469000	Weak transcription	HSMMtube	muscle
19	chr4:74465400-74469000	Weak transcription	Osteobl	bone
20	chr4:74465400-74469200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:74465400-74469200	Enhancers	HepG2	liver
22	chr4:74465400-74469600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:74465400-74483000	Weak transcription	Esophagus	oesophagus
24	chr4:74465600-74467200	Enhancers	Dnd41	blood
25	chr4:74465600-74469000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:74465600-74469000	Weak transcription	GM12878-XiMat	blood
27	chr4:74465600-74469200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:74465600-74472200	Weak transcription	HMEC	breast
29	chr4:74465800-74467600	Weak transcription	Pancreas	Pancrea
30	chr4:74465800-74468000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:74465800-74469000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:74465800-74471000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:74465800-74471800	Weak transcription	Small Intestine	intestine
34	chr4:74465800-74472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:74465800-74473000	Weak transcription	NHEK	skin
36	chr4:74465800-74476000	Weak transcription	Placenta	Placenta
37	chr4:74466000-74468600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:74466000-74469000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:74466200-74466600	Active TSS	Thymus	Thymus
40	chr4:74466200-74467800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:74466400-74466600	Flanking Active TSS	A549	lung
42	chr4:74466400-74467000	Enhancers	Rectal Smooth Muscle	rectum
43	chr4:74466400-74467200	Enhancers	Fetal Lung	lung
44	chr4:74466400-74467600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:74466400-74469000	Weak transcription	HSMM	muscle

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